This document has last been compiled on 2021-12-10 17:59:02.
## Reading in metadata from file: results/Year123/data/leaf_meta.txt
## Reading in data from file: results/Year123/data/leaf_normCounts.txt## Reading in metadata from file: results/Year123/data/root_meta.txt
## Reading in data from file: results/Year123/data/root_normCounts.txt## Total number of leaf samples: 750
## Total number of genes in leaf samples: 23113
## No additional bad samples to remove (probably removed during normalization)
## Removing the 72 samples identified as not part of the main experiment, from the leaf samples
## After filtering leaf samples: 678 samples, 23113 genes## Total number of root samples: 758
## Total number of genes in root samples: 24939
## No additional bad samples to remove (probably removed during normalization)
## Removing the 72 samples identified as not part of the main experiment, from the root samples
## After filtering root samples: 686 samples, 24939 genesThis analysis looks specifically at finding genes that have large, differential changes from time point to time point.
The analysis is done on root and leaf separately. We run the model with a fixed effect for each TP/condition/etc. and then query the following contrast for each time point (TP) i and Treatment (i.e. preflowering vs postflowering):
(TP i - TP (i-1))[430 Treatment] - (TP i - TP (i-1))[430 Control] (TP i - TP (i-1))[642 Treatment] - (TP i - TP (i-1))[642 Control]
To be able to further evaluate/filter these quantities, we also just test whether the individual differences are significant, i.e. whether the change in treatment is significant or the change in control is significant.
(TP i - TP (i-1))[430 Treatment] (TP i - TP (i-1))[430 Control] (TP i - TP (i-1))[642 Treatment] (TP i - TP (i-1))[642 Control]
This is to allow us to find those that are different combinations in the change in treatment and control.
We also do these same comparisons, controlling for genotype.
p-values are corrected using BH across all contrasts within a contrast group (4 different groups of contrasts, described above). Genes with a p-value smaller than 0.05 are considered as differentially expressed.
We calculate the difference for every pair of time points, but the interest is in particular pairs of time points, when drought starts or water is turned back on.
We calculate both the time point and the genotype difference with our function moaninDeJumpsContrast_tpDiff and moaninDeJumpsContrast_genoTPDiff for leaf and root, pre and post. Note that we calculate (and later save) the results for all genes.
We determine the direction of the change (“+/-”), with “0” if the change is not significant. This creates variables ‘DirectionTreat’, ‘DirectionCtrl’ and ‘Direction’ (where the last is the combination of the first two).
In this report, Treat refers to the difference of the time point with the previous time point for treatment (i.e. drought), while Control columns are those on control. Combined refers to the difference of these differences (the one of relevance, because if control is also showing the same change between the time points, that is not of interest.)
(This is done for the tpDiff matrix, i.e. not the genotype difference results)
# DE_Jump for leaf, root, Preflowering, and Postflowering, with genotypes BT642 and RT430
tpDiff_leaf_pre <- moaninDeJumpsContrast_tpDiff("leaf","Preflowering",timepoints_before=timepoints_before_leaf_pre,timepoints_after=timepoints_after_leaf_pre)## Sample type: leaf , Treat: Preflowering
## Saving leaf preflowering results in results/Year123/DE_jumpstpDiff_leaf_post <- moaninDeJumpsContrast_tpDiff("leaf","Postflowering",timepoints_before=timepoints_before_leaf_post,timepoints_after=timepoints_after_leaf_post)## Sample type: leaf , Treat: Postflowering
## Saving leaf postflowering results in results/Year123/DE_jumpstpDiff_root_pre <- moaninDeJumpsContrast_tpDiff("root","Preflowering",timepoints_before=timepoints_before_root_pre,timepoints_after=timepoints_after_root_pre)## Sample type: root , Treat: Preflowering
## Saving root preflowering results in results/Year123/DE_jumpstpDiff_root_post <- moaninDeJumpsContrast_tpDiff("root","Postflowering",timepoints_before=timepoints_before_root_post,timepoints_after=timepoints_after_root_post)## Sample type: root , Treat: Postflowering
## Saving root postflowering results in results/Year123/DE_jumps# DE_Jump for leaf, root, Preflowering, and Postflowering, with genotype GenoDiff
if(! typeyear %in% c("BT642", "RT430")){
genoTPDiff_leaf_pre <- moaninDeJumpsContrast_genoTPDiff("leaf","Preflowering",timepoints_before=timepoints_before_leaf_pre,timepoints_after=timepoints_after_leaf_pre)
genoTPDiff_leaf_post <- moaninDeJumpsContrast_genoTPDiff("leaf","Postflowering",timepoints_before=timepoints_before_leaf_post,timepoints_after=timepoints_after_leaf_post)
genoTPDiff_root_pre <- moaninDeJumpsContrast_genoTPDiff("root","Preflowering",timepoints_before=timepoints_before_root_pre,timepoints_after=timepoints_after_root_pre)
genoTPDiff_root_post <- moaninDeJumpsContrast_genoTPDiff("root","Postflowering",timepoints_before=timepoints_before_root_post,timepoints_after=timepoints_after_root_post)
}## Sample type: leaf , Treat: Preflowering
## Saving leaf preflowering results of genotype differences in results/Year123/DE_jumps
## Sample type: leaf , Treat: Postflowering
## Saving leaf postflowering results of genotype differences in results/Year123/DE_jumps
## Sample type: root , Treat: Preflowering
## Saving root preflowering results of genotype differences in results/Year123/DE_jumps
## Sample type: root , Treat: Postflowering
## Saving root postflowering results of genotype differences in results/Year123/DE_jumpsFirst we write all moanin results per timpoint and the combined results to a comma-deliminated file in results/Year123/DE_jumps,
leaf_Preflowering_jumpDE_all.csv
leaf_GenoDiff_Preflowering_jumpDE_all.csv
and similarly for root.
Note on significance: not all TPs have replication, reducing their ability to be significant, and further some TPs could have no data (e.g. they only had a single replicate, but that replicate was not processed). Also, the first drought time point in preflowering is compared to the control plot, so that the difference of the differences is just the difference between control and treatment in TP[i]. Here is a table of the replication at each time point, condition and genotype:
## , , = BT642
##
##
## Control Postflowering Preflowering
## Day007 3 0 0
## Day014 7 0 5
## Day021 9 0 8
## Day028 7 0 9
## Day035 9 0 8
## Day042 8 0 9
## Day049 7 0 6
## Day056 9 0 9
## Day058 6 0 6
## Day059 5 0 6
## Day061 5 0 5
## Day063 9 9 9
## Day065 5 4 0
## Day066 3 3 0
## Day068 3 3 0
## Day070 9 9 9
## Day077 9 9 9
## Day084 9 7 9
## Day091 9 9 9
## Day098 1 1 1
## Day105 8 9 9
## Day112 0 1 1
## Day119 3 3 3
##
## , , = RT430
##
##
## Control Postflowering Preflowering
## Day007 3 0 0
## Day014 7 0 5
## Day021 9 0 6
## Day028 9 0 9
## Day035 9 0 7
## Day042 9 0 9
## Day049 7 0 7
## Day056 9 0 9
## Day058 6 0 6
## Day059 6 0 5
## Day061 5 0 6
## Day063 8 9 9
## Day065 6 4 0
## Day066 3 3 0
## Day068 3 3 0
## Day070 9 9 9
## Day077 9 9 8
## Day084 9 7 9
## Day091 9 9 9
## Day098 1 1 1
## Day105 8 8 7
## Day112 1 0 1
## Day119 3 3 3In determining significance in the tables that follow, we count a gene as significant if it both has a significant difference in the treatment from TP[i] to TP[i-1] and that difference is significantly different from that seen in control (the difference of the differences is significant). For these summaries, we use the tpAdj, i.e. multiple testing correction done within each timepoint/contrast pair, but not more agressively across all the timepoints within a contrast (groupAdj).
## Example lines of results after subsetting to the significant genes## timepoints Gene Genotype lfc pval
## 235 Day021-Day014 Sobic.001G029300.v3.1 BT642 0.6683036 1.429034e-03
## 739 Day021-Day014 Sobic.001G093000.v3.1 BT642 1.2215458 3.683286e-04
## 1813 Day021-Day014 Sobic.001G243732.v3.1 BT642 0.4981227 1.337904e-03
## 2344 Day021-Day014 Sobic.001G319900.v3.1 BT642 1.3395852 6.218690e-04
## 2500 Day021-Day014 Sobic.001G343400.v3.1 BT642 2.2565142 6.592395e-06
## 3368 Day021-Day014 Sobic.001G452100.v3.1 BT642 -0.8155283 2.892962e-04
## qval Treat.lfc Treat.pval Treat.tpAdj.pval Ctrl.lfc
## 235 0.0428951397 -0.9168824 8.153293e-09 2.479566e-06 -1.58518603
## 739 0.0164664990 0.8133580 1.118078e-03 4.647865e-02 -0.40818774
## 1813 0.0409262622 0.4273969 2.054128e-04 1.474443e-02 -0.07072572
## 2344 0.0238362491 1.1243935 5.082453e-05 4.834187e-03 -0.21519165
## 2500 0.0007290431 1.6028373 3.107291e-05 3.309623e-03 -0.65367699
## 3368 0.0138436912 -0.7682202 4.644499e-06 6.925698e-04 0.04730814
## Ctrl.pval Ctrl.tpAdj.pval DirectionTreat DirectionCtrl Direction
## 235 1.079594e-27 2.079387e-24 Treat- Ctrl- Treat-.Ctrl-
## 739 8.078482e-02 2.196165e-01 Treat+ Ctrl0 Treat+.Ctrl0
## 1813 4.957860e-01 7.076998e-01 Treat+ Ctrl0 Treat+.Ctrl0
## 2344 4.341046e-01 6.544129e-01 Treat+ Ctrl0 Treat+.Ctrl0
## 2500 3.910427e-02 1.307698e-01 Treat+ Ctrl0 Treat+.Ctrl0
## 3368 7.517411e-01 8.869305e-01 Treat- Ctrl0 Treat-.Ctrl0## Example lines of results after subsetting to the significant genes, at the water change## timepoints Gene Genotype lfc pval
## 138697 Day058-Day056 Sobic.001G002800.v3.1 BT642 -1.5836006 2.644956e-03
## 138711 Day058-Day056 Sobic.001G004500.v3.1 BT642 1.9289053 2.037074e-03
## 138715 Day058-Day056 Sobic.001G005300.v3.1 BT642 4.1084048 1.073501e-12
## 138723 Day058-Day056 Sobic.001G006400.v3.1 BT642 1.1694171 1.347679e-05
## 138738 Day058-Day056 Sobic.001G007900.v3.1 BT642 0.5510538 3.131052e-03
## 138760 Day058-Day056 Sobic.001G010300.v3.1 BT642 -0.4302999 2.139181e-03
## qval Treat.lfc Treat.pval Treat.tpAdj.pval Ctrl.lfc
## 138697 3.313435e-02 -1.3455602 6.448255e-04 4.149179e-03 0.23804041
## 138711 2.800885e-02 2.3998210 3.328614e-09 1.739682e-07 0.47091574
## 138715 1.908601e-09 3.8102228 1.114891e-19 1.288423e-16 -0.29818199
## 138723 9.643624e-04 1.2021083 5.414936e-10 3.575869e-08 0.03269111
## 138738 3.711180e-02 0.6151518 2.636693e-06 4.537743e-05 0.06409809
## 138760 2.877705e-02 -0.4755957 2.692731e-06 4.613573e-05 -0.04529576
## Ctrl.pval Ctrl.tpAdj.pval DirectionTreat DirectionCtrl Direction
## 138697 0.4964242 0.9999905 Treat- Ctrl0 Treat-.Ctrl0
## 138711 0.3251008 0.9999905 Treat+ Ctrl0 Treat+.Ctrl0
## 138715 0.4491139 0.9999905 Treat+ Ctrl0 Treat+.Ctrl0
## 138723 0.8613347 0.9999905 Treat+ Ctrl0 Treat+.Ctrl0
## 138738 0.6310292 0.9999905 Treat+ Ctrl0 Treat+.Ctrl0
## 138760 0.6419479 0.9999905 Treat- Ctrl0 Treat-.Ctrl0## Example lines of results after subsetting to the significant genes, only water change at Day063-Day056## timepoints Gene Genotype lfc pval
## 346714 Day063-Day056 Sobic.001G002800.v3.1 BT642 -1.9638437 3.274705e-05
## 346732 Day063-Day056 Sobic.001G005300.v3.1 BT642 2.7518772 6.769793e-08
## 346742 Day063-Day056 Sobic.001G006600.v3.1 BT642 -0.9563068 7.873631e-07
## 346747 Day063-Day056 Sobic.001G007100.v3.1 BT642 -0.4556977 2.813767e-03
## 346767 Day063-Day056 Sobic.001G009300.v3.1 BT642 0.4619269 1.166191e-03
## 346805 Day063-Day056 Sobic.001G013500.v3.1 BT642 -0.6213303 1.367335e-03
## qval Treat.lfc Treat.pval Treat.tpAdj.pval Ctrl.lfc
## 346714 2.259351e-03 -1.5618349 7.835373e-06 1.629269e-04 0.402008796
## 346732 2.059879e-05 2.7585651 1.432419e-13 5.517918e-11 0.006687912
## 346742 1.467607e-04 -0.6155261 8.970807e-06 1.820389e-04 0.340780763
## 346747 4.774933e-02 -0.3247014 2.472991e-03 1.452560e-02 0.130996298
## 346767 2.628022e-02 0.4380327 1.467370e-05 2.704570e-04 -0.023894159
## 346805 2.926223e-02 -0.4466716 1.159832e-03 8.148441e-03 0.174658721
## Ctrl.pval Ctrl.tpAdj.pval DirectionTreat DirectionCtrl Direction
## 346714 0.20442566 1 Treat- Ctrl0 Treat-.Ctrl0
## 346732 0.98464392 1 Treat+ Ctrl0 Treat+.Ctrl0
## 346742 0.01089435 1 Treat- Ctrl0 Treat-.Ctrl0
## 346747 0.22555021 1 Treat- Ctrl0 Treat-.Ctrl0
## 346767 0.81117340 1 Treat+ Ctrl0 Treat+.Ctrl0
## 346805 0.20059488 1 Treat- Ctrl0 Treat-.Ctrl0We show the tabulatation of the number of significant differences in each TP by genotype. Here the TP refers to the difference of that TP with the TP before it.
In leaf:
## Leaf, Pre##
## BT642 RT430
## Day021-Day014 29 46
## Day028-Day021 0 0
## Day035-Day028 72 5
## Day042-Day035 0 0
## Day049-Day042 0 0
## Day056-Day049 0 1
## Day058-Day056 2207 814
## Day059-Day058 5 8
## Day061-Day059 1 6
## Day063-Day056 1383 1640
## Day063-Day061 0 0
## Day077-Day070 0 0
## Day084-Day077 0 0
## Day091-Day084 0 0
## Day098-Day091 0 0
## Day105-Day098 0 0
## Day112-Day105 0 7
## Day119-Day112 0 4## Leaf, Post##
## BT642 RT430
## Day065-Day063 0 0
## Day066-Day065 0 0
## Day068-Day066 0 0
## Day070-Day063 1 19
## Day070-Day065 0 0
## Day070-Day068 0 0
## Day077-Day070 13 60
## Day084-Day077 4 1
## Day091-Day084 2 0
## Day098-Day091 0 0
## Day105-Day098 0 1We can repeat this with the root
## root, Pre##
## BT642 RT430
## Day021-Day014 1 59
## Day028-Day021 2 162
## Day035-Day028 90 92
## Day042-Day035 1 0
## Day049-Day042 0 0
## Day056-Day049 1 0
## Day058-Day056 7324 6039
## Day059-Day058 89 42
## Day061-Day059 155 92
## Day063-Day056 5727 6521
## Day063-Day061 103 6
## Day077-Day070 0 0
## Day084-Day077 0 1
## Day091-Day084 1 0
## Day098-Day091 0 0
## Day105-Day098 0 0
## Day112-Day105 0 4
## Day119-Day112 0 9## root, Post##
## BT642 RT430
## Day065-Day063 172 0
## Day066-Day065 0 0
## Day068-Day066 0 1
## Day070-Day063 1828 1337
## Day070-Day065 0 7
## Day070-Day068 2 4
## Day077-Day070 38 52
## Day084-Day077 0 5
## Day091-Day084 0 6
## Day098-Day091 0 51
## Day105-Day098 0 55
## Day112-Day105 0 1
## Day119-Day112 0 0We can further look at the direction of the change in treatment, where the direction is defined as above to either be an increase or a decrease (sign of the logFR of the treatment difference between the tps), and further categorized to be the same direction or opposite as the change
Leaf:
## Leaf, Pre## , , = BT642
##
##
## Treat-.Ctrl- Treat-.Ctrl+ Treat-.Ctrl0 Treat+.Ctrl-
## Day021-Day014 3 0 11 0
## Day028-Day021 0 0 0 0
## Day035-Day028 0 0 21 0
## Day042-Day035 0 0 0 0
## Day049-Day042 0 0 0 0
## Day056-Day049 0 0 0 0
## Day058-Day056 0 0 950 0
## Day059-Day058 0 0 0 0
## Day061-Day059 0 0 1 0
## Day063-Day056 0 0 898 0
## Day063-Day061 0 0 0 0
## Day077-Day070 0 0 0 0
## Day084-Day077 0 0 0 0
## Day091-Day084 0 0 0 0
## Day098-Day091 0 0 0 0
## Day105-Day098 0 0 0 0
## Day112-Day105 0 0 0 0
## Day119-Day112 0 0 0 0
##
## Treat+.Ctrl+ Treat+.Ctrl0
## Day021-Day014 0 15
## Day028-Day021 0 0
## Day035-Day028 0 51
## Day042-Day035 0 0
## Day049-Day042 0 0
## Day056-Day049 0 0
## Day058-Day056 0 1257
## Day059-Day058 0 5
## Day061-Day059 0 0
## Day063-Day056 0 485
## Day063-Day061 0 0
## Day077-Day070 0 0
## Day084-Day077 0 0
## Day091-Day084 0 0
## Day098-Day091 0 0
## Day105-Day098 0 0
## Day112-Day105 0 0
## Day119-Day112 0 0
##
## , , = RT430
##
##
## Treat-.Ctrl- Treat-.Ctrl+ Treat-.Ctrl0 Treat+.Ctrl-
## Day021-Day014 2 0 23 2
## Day028-Day021 0 0 0 0
## Day035-Day028 0 0 0 0
## Day042-Day035 0 0 0 0
## Day049-Day042 0 0 0 0
## Day056-Day049 0 0 0 0
## Day058-Day056 0 2 483 0
## Day059-Day058 0 0 0 0
## Day061-Day059 0 0 6 0
## Day063-Day056 0 2 1006 4
## Day063-Day061 0 0 0 0
## Day077-Day070 0 0 0 0
## Day084-Day077 0 0 0 0
## Day091-Day084 0 0 0 0
## Day098-Day091 0 0 0 0
## Day105-Day098 0 0 0 0
## Day112-Day105 0 0 3 0
## Day119-Day112 0 0 4 0
##
## Treat+.Ctrl+ Treat+.Ctrl0
## Day021-Day014 1 18
## Day028-Day021 0 0
## Day035-Day028 0 5
## Day042-Day035 0 0
## Day049-Day042 0 0
## Day056-Day049 0 1
## Day058-Day056 2 327
## Day059-Day058 0 8
## Day061-Day059 0 0
## Day063-Day056 0 628
## Day063-Day061 0 0
## Day077-Day070 0 0
## Day084-Day077 0 0
## Day091-Day084 0 0
## Day098-Day091 0 0
## Day105-Day098 0 0
## Day112-Day105 0 4
## Day119-Day112 0 0## Leaf, Post## , , = BT642
##
##
## Treat-.Ctrl0 Treat+.Ctrl0
## Day065-Day063 0 0
## Day066-Day065 0 0
## Day068-Day066 0 0
## Day070-Day063 0 1
## Day070-Day065 0 0
## Day070-Day068 0 0
## Day077-Day070 6 7
## Day084-Day077 2 2
## Day091-Day084 2 0
## Day098-Day091 0 0
## Day105-Day098 0 0
##
## , , = RT430
##
##
## Treat-.Ctrl0 Treat+.Ctrl0
## Day065-Day063 0 0
## Day066-Day065 0 0
## Day068-Day066 0 0
## Day070-Day063 4 15
## Day070-Day065 0 0
## Day070-Day068 0 0
## Day077-Day070 5 55
## Day084-Day077 1 0
## Day091-Day084 0 0
## Day098-Day091 0 0
## Day105-Day098 1 0Root:
## root, Pre## , , = BT642
##
##
## Treat-.Ctrl- Treat-.Ctrl+ Treat-.Ctrl0 Treat+.Ctrl-
## Day021-Day014 0 1 0 0
## Day028-Day021 0 2 0 0
## Day035-Day028 0 0 27 13
## Day042-Day035 0 0 0 0
## Day049-Day042 0 0 0 0
## Day056-Day049 0 0 1 0
## Day058-Day056 80 16 2937 10
## Day059-Day058 0 0 42 0
## Day061-Day059 0 0 82 0
## Day063-Day056 0 0 3136 0
## Day063-Day061 0 0 68 0
## Day077-Day070 0 0 0 0
## Day084-Day077 0 0 0 0
## Day091-Day084 0 0 0 0
## Day098-Day091 0 0 0 0
## Day105-Day098 0 0 0 0
## Day112-Day105 0 0 0 0
## Day119-Day112 0 0 0 0
##
## Treat+.Ctrl+ Treat+.Ctrl0
## Day021-Day014 0 0
## Day028-Day021 0 0
## Day035-Day028 0 50
## Day042-Day035 0 1
## Day049-Day042 0 0
## Day056-Day049 0 0
## Day058-Day056 109 4172
## Day059-Day058 0 47
## Day061-Day059 0 73
## Day063-Day056 0 2591
## Day063-Day061 0 35
## Day077-Day070 0 0
## Day084-Day077 0 0
## Day091-Day084 0 1
## Day098-Day091 0 0
## Day105-Day098 0 0
## Day112-Day105 0 0
## Day119-Day112 0 0
##
## , , = RT430
##
##
## Treat-.Ctrl- Treat-.Ctrl+ Treat-.Ctrl0 Treat+.Ctrl-
## Day021-Day014 0 0 31 5
## Day028-Day021 1 10 70 12
## Day035-Day028 0 0 27 1
## Day042-Day035 0 0 0 0
## Day049-Day042 0 0 0 0
## Day056-Day049 0 0 0 0
## Day058-Day056 42 11 2363 12
## Day059-Day058 0 0 6 0
## Day061-Day059 0 0 39 3
## Day063-Day056 2 153 2970 202
## Day063-Day061 0 0 6 0
## Day077-Day070 0 0 0 0
## Day084-Day077 0 0 0 0
## Day091-Day084 0 0 0 0
## Day098-Day091 0 0 0 0
## Day105-Day098 0 0 0 0
## Day112-Day105 0 0 1 0
## Day119-Day112 0 3 5 0
##
## Treat+.Ctrl+ Treat+.Ctrl0
## Day021-Day014 0 23
## Day028-Day021 0 69
## Day035-Day028 0 64
## Day042-Day035 0 0
## Day049-Day042 0 0
## Day056-Day049 0 0
## Day058-Day056 121 3490
## Day059-Day058 0 36
## Day061-Day059 0 50
## Day063-Day056 3 3191
## Day063-Day061 0 0
## Day077-Day070 0 0
## Day084-Day077 0 1
## Day091-Day084 0 0
## Day098-Day091 0 0
## Day105-Day098 0 0
## Day112-Day105 0 3
## Day119-Day112 0 1## root, Post## , , = BT642
##
##
## Treat-.Ctrl+ Treat-.Ctrl0 Treat+.Ctrl- Treat+.Ctrl+
## Day065-Day063 1 100 4 0
## Day066-Day065 0 0 0 0
## Day068-Day066 0 0 0 0
## Day070-Day063 0 1183 0 0
## Day070-Day065 0 0 0 0
## Day070-Day068 0 2 0 0
## Day077-Day070 0 26 0 0
## Day084-Day077 0 0 0 0
## Day091-Day084 0 0 0 0
## Day098-Day091 0 0 0 0
## Day105-Day098 0 0 0 0
## Day112-Day105 0 0 0 0
## Day119-Day112 0 0 0 0
##
## Treat+.Ctrl0
## Day065-Day063 67
## Day066-Day065 0
## Day068-Day066 0
## Day070-Day063 645
## Day070-Day065 0
## Day070-Day068 0
## Day077-Day070 12
## Day084-Day077 0
## Day091-Day084 0
## Day098-Day091 0
## Day105-Day098 0
## Day112-Day105 0
## Day119-Day112 0
##
## , , = RT430
##
##
## Treat-.Ctrl+ Treat-.Ctrl0 Treat+.Ctrl- Treat+.Ctrl+
## Day065-Day063 0 0 0 0
## Day066-Day065 0 0 0 0
## Day068-Day066 0 1 0 0
## Day070-Day063 0 1015 0 0
## Day070-Day065 0 4 0 0
## Day070-Day068 0 3 0 0
## Day077-Day070 1 18 0 1
## Day084-Day077 0 1 0 0
## Day091-Day084 0 1 0 0
## Day098-Day091 0 1 0 0
## Day105-Day098 0 54 0 0
## Day112-Day105 0 0 0 0
## Day119-Day112 0 0 0 0
##
## Treat+.Ctrl0
## Day065-Day063 0
## Day066-Day065 0
## Day068-Day066 0
## Day070-Day063 322
## Day070-Day065 3
## Day070-Day068 1
## Day077-Day070 32
## Day084-Day077 4
## Day091-Day084 5
## Day098-Day091 50
## Day105-Day098 1
## Day112-Day105 1
## Day119-Day112 0## Example lines of results after subsetting to the significant genes, only water change at Day063-Day056## timepoints Gene Genotype lfc pval
## 346714 Day063-Day056 Sobic.001G002800.v3.1 BT642 -1.9638437 3.274705e-05
## 346732 Day063-Day056 Sobic.001G005300.v3.1 BT642 2.7518772 6.769793e-08
## 346742 Day063-Day056 Sobic.001G006600.v3.1 BT642 -0.9563068 7.873631e-07
## 346747 Day063-Day056 Sobic.001G007100.v3.1 BT642 -0.4556977 2.813767e-03
## 346767 Day063-Day056 Sobic.001G009300.v3.1 BT642 0.4619269 1.166191e-03
## 346805 Day063-Day056 Sobic.001G013500.v3.1 BT642 -0.6213303 1.367335e-03
## qval Treat.lfc Treat.pval Treat.tpAdj.pval Ctrl.lfc
## 346714 2.259351e-03 -1.5618349 7.835373e-06 1.629269e-04 0.402008796
## 346732 2.059879e-05 2.7585651 1.432419e-13 5.517918e-11 0.006687912
## 346742 1.467607e-04 -0.6155261 8.970807e-06 1.820389e-04 0.340780763
## 346747 4.774933e-02 -0.3247014 2.472991e-03 1.452560e-02 0.130996298
## 346767 2.628022e-02 0.4380327 1.467370e-05 2.704570e-04 -0.023894159
## 346805 2.926223e-02 -0.4466716 1.159832e-03 8.148441e-03 0.174658721
## Ctrl.pval Ctrl.tpAdj.pval DirectionTreat DirectionCtrl Direction
## 346714 0.20442566 1 Treat- Ctrl0 Treat-.Ctrl0
## 346732 0.98464392 1 Treat+ Ctrl0 Treat+.Ctrl0
## 346742 0.01089435 1 Treat- Ctrl0 Treat-.Ctrl0
## 346747 0.22555021 1 Treat- Ctrl0 Treat-.Ctrl0
## 346767 0.81117340 1 Treat+ Ctrl0 Treat+.Ctrl0
## 346805 0.20059488 1 Treat- Ctrl0 Treat-.Ctrl0We repeat the signsummarization for the genotype specific results
## Example lines of results after subsetting to the significant genes## timepoints Gene Genotype lfc pval
## 19999 Day021-Day014 Sobic.009G119800.v3.1 Both -1.597084 9.371335e-10
## 68139 Day035-Day028 Sobic.010G119200.v3.1 Both -1.556352 1.602995e-06
## 142216 Day058-Day056 Sobic.001G473100.v3.1 Both -1.434740 1.248294e-04
## 143491 Day058-Day056 Sobic.002G121800.v3.1 Both 1.021032 5.033572e-07
## 145503 Day058-Day056 Sobic.002G396600.v3.1 Both -2.536171 1.521916e-05
## 151588 Day058-Day056 Sobic.004G336401.v3.1 Both 1.247768 1.568980e-08
## qval Treat.lfc Treat.pval Treat.tpAdj.pval Ctrl.lfc
## 19999 2.165997e-05 -0.8125623 2.208788e-05 4.671904e-02 0.78452130
## 68139 3.705003e-02 -1.3017752 9.324163e-08 1.077547e-03 0.25457666
## 142216 3.580687e-02 -1.2618537 3.301839e-06 1.659031e-03 0.17288632
## 143491 4.653638e-04 0.9692676 5.658309e-11 1.307805e-07 -0.05176430
## 145503 6.897263e-03 -3.0065891 2.598219e-13 1.201052e-09 -0.47041852
## 151588 4.029315e-05 1.3423047 2.100637e-16 4.855202e-12 0.09453634
## Ctrl.pval Ctrl.tpAdj.pval DirectionTreat DirectionCtrl Direction
## 19999 6.527798e-06 0.004077756 Treat- Ctrl+ Treat-.Ctrl+
## 68139 2.310874e-01 0.990094363 Treat- Ctrl0 Treat-.Ctrl0
## 142216 5.005735e-01 1.000000000 Treat- Ctrl0 Treat-.Ctrl0
## 143491 7.095122e-01 1.000000000 Treat+ Ctrl0 Treat+.Ctrl0
## 145503 2.637134e-01 1.000000000 Treat- Ctrl0 Treat-.Ctrl0
## 151588 5.259939e-01 1.000000000 Treat+ Ctrl0 Treat+.Ctrl0## Example lines of results after subsetting to the significant genes, only at the water change## timepoints Gene Genotype lfc pval
## 142216 Day058-Day056 Sobic.001G473100.v3.1 Both -1.434740 1.248294e-04
## 143491 Day058-Day056 Sobic.002G121800.v3.1 Both 1.021032 5.033572e-07
## 145503 Day058-Day056 Sobic.002G396600.v3.1 Both -2.536171 1.521916e-05
## 151588 Day058-Day056 Sobic.004G336401.v3.1 Both 1.247768 1.568980e-08
## 152651 Day058-Day056 Sobic.005G152600.v3.1 Both 2.775047 2.832620e-07
## 152760 Day058-Day056 Sobic.005G171200.v3.1 Both -1.571786 4.414010e-05
## qval Treat.lfc Treat.pval Treat.tpAdj.pval Ctrl.lfc
## 142216 3.580687e-02 -1.2618537 3.301839e-06 1.659031e-03 0.172886315
## 143491 4.653638e-04 0.9692676 5.658309e-11 1.307805e-07 -0.051764301
## 145503 6.897263e-03 -3.0065891 2.598219e-13 1.201052e-09 -0.470418522
## 151588 4.029315e-05 1.3423047 2.100637e-16 4.855202e-12 0.094536337
## 152651 2.975924e-04 1.6182112 2.312452e-05 7.977269e-03 -1.156835881
## 152760 1.500309e-02 -1.5749791 5.212299e-09 7.086581e-06 -0.003192658
## Ctrl.pval Ctrl.tpAdj.pval DirectionTreat DirectionCtrl Direction
## 142216 0.500573550 1.000000 Treat- Ctrl0 Treat-.Ctrl0
## 143491 0.709512209 1.000000 Treat+ Ctrl0 Treat+.Ctrl0
## 145503 0.263713432 1.000000 Treat- Ctrl0 Treat-.Ctrl0
## 151588 0.525993895 1.000000 Treat+ Ctrl0 Treat+.Ctrl0
## 152651 0.002196101 0.512712 Treat+ Ctrl0 Treat+.Ctrl0
## 152760 0.990721764 1.000000 Treat- Ctrl0 Treat-.Ctrl0Year1: There are very few found significant in this genotype analysis except in root in pre-flowering. This is not surprising in post-flowering in leaf, in particular, where almost non of the drought tolerant are found due to variability in week 10 amongst the replicates.
We show the tabulatation of the number of significant differences in each TP by genotype.
Leaf:
## Leaf, Pre##
## Day021-Day014 Day028-Day021 Day035-Day028 Day042-Day035 Day049-Day042
## FALSE 23112 23113 23112 23113 23113
## TRUE 1 0 1 0 0
##
## Day056-Day049 Day058-Day056 Day059-Day058 Day061-Day059 Day063-Day056
## FALSE 23113 23026 23113 23113 23079
## TRUE 0 87 0 0 34
##
## Day063-Day061 Day077-Day070 Day084-Day077 Day091-Day084 Day098-Day091
## FALSE 23113 23113 23113 23113 23113
## TRUE 0 0 0 0 0
##
## Day105-Day098
## FALSE 23113
## TRUE 0## Leaf, Post##
## Day065-Day063 Day066-Day065 Day068-Day066 Day070-Day063 Day070-Day065
## FALSE 23113 23113 23113 23113 23113
## TRUE 0 0 0 0 0
##
## Day070-Day068 Day077-Day070 Day084-Day077 Day091-Day084 Day098-Day091
## FALSE 23113 23111 23113 23113 23113
## TRUE 0 2 0 0 0
##
## Day105-Day098
## FALSE 23113
## TRUE 0Root:
## Root, Pre##
## Day021-Day014 Day028-Day021 Day035-Day028 Day042-Day035 Day049-Day042
## FALSE 24939 24938 24939 24939 24939
## TRUE 0 1 0 0 0
##
## Day056-Day049 Day058-Day056 Day059-Day058 Day061-Day059 Day063-Day056
## FALSE 24939 24862 24938 24934 24897
## TRUE 0 77 1 5 42
##
## Day063-Day061 Day077-Day070 Day084-Day077 Day091-Day084 Day098-Day091
## FALSE 24939 24939 24939 24939 24939
## TRUE 0 0 0 0 0
##
## Day105-Day098
## FALSE 24939
## TRUE 0## Root, Post##
## Day065-Day063 Day066-Day065 Day068-Day066 Day070-Day063 Day070-Day065
## FALSE 24939 24939 24571 24937 24939
## TRUE 0 0 368 2 0
##
## Day070-Day068 Day077-Day070 Day084-Day077 Day091-Day084 Day098-Day091
## FALSE 24141 24938 24939 24939 24926
## TRUE 798 1 0 0 13
##
## Day105-Day098
## FALSE 24928
## TRUE 11## [1] "2021-12-10 18:58:17 PST"## R version 4.1.2 (2021-11-01)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] forcats_0.5.1 stringr_1.4.0
## [3] purrr_0.3.4 readr_2.0.2
## [5] tidyr_1.1.4 tibble_3.1.6
## [7] ggplot2_3.3.5 tidyverse_1.3.1
## [9] moanin_1.1.2 topGO_2.44.0
## [11] SparseM_1.81 GO.db_3.13.0
## [13] AnnotationDbi_1.56.1 graph_1.72.0
## [15] SummarizedExperiment_1.24.0 Biobase_2.54.0
## [17] GenomicRanges_1.46.0 GenomeInfoDb_1.30.0
## [19] IRanges_2.28.0 S4Vectors_0.32.2
## [21] BiocGenerics_0.40.0 MatrixGenerics_1.6.0
## [23] matrixStats_0.61.0 dplyr_1.0.7
## [25] rmarkdown_2.11 knitr_1.36
## [27] SCF_4.1.0
##
## loaded via a namespace (and not attached):
## [1] fs_1.5.0 bitops_1.0-7 lubridate_1.8.0
## [4] bit64_4.0.5 httr_1.4.2 tools_4.1.2
## [7] backports_1.3.0 bslib_0.3.1 utf8_1.2.2
## [10] R6_2.5.1 DBI_1.1.1 colorspace_2.0-2
## [13] withr_2.4.2 tidyselect_1.1.1 gridExtra_2.3
## [16] bit_4.0.4 compiler_4.1.2 cli_3.1.0
## [19] rvest_1.0.2 xml2_1.3.2 DelayedArray_0.20.0
## [22] sass_0.4.0 scales_1.1.1 digest_0.6.28
## [25] XVector_0.34.0 pkgconfig_2.0.3 htmltools_0.5.2
## [28] dbplyr_2.1.1 fastmap_1.1.0 limma_3.50.0
## [31] readxl_1.3.1 rlang_0.4.12 rstudioapi_0.13
## [34] RSQLite_2.2.8 jquerylib_0.1.4 generics_0.1.1
## [37] jsonlite_1.7.2 gtools_3.9.2 RCurl_1.98-1.5
## [40] magrittr_2.0.1 GenomeInfoDbData_1.2.7 Matrix_1.3-4
## [43] Rcpp_1.0.7 munsell_0.5.0 fansi_0.5.0
## [46] viridis_0.6.2 lifecycle_1.0.1 stringi_1.7.5
## [49] yaml_2.2.1 edgeR_3.36.0 ClusterR_1.2.5
## [52] zlibbioc_1.40.0 grid_4.1.2 blob_1.2.2
## [55] crayon_1.4.2 lattice_0.20-45 haven_2.4.3
## [58] Biostrings_2.60.2 splines_4.1.2 hms_1.1.1
## [61] KEGGREST_1.34.0 locfit_1.5-9.4 pillar_1.6.4
## [64] reprex_2.0.1 glue_1.5.0 evaluate_0.14
## [67] modelr_0.1.8 tzdb_0.2.0 png_0.1-7
## [70] vctrs_0.3.8 cellranger_1.1.0 gtable_0.3.0
## [73] assertthat_0.2.1 cachem_1.0.6 xfun_0.28
## [76] broom_0.7.10 viridisLite_0.4.0 memoise_2.0.0
## [79] gmp_0.6-2.1 ellipsis_0.3.2