Last updated: 2020-12-11
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Knit directory: R_gene_analysis/
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| html | 83dc49a | Philipp Bayer | 2020-12-11 | Trace deleted files |
| Rmd | dae157b | Philipp Bayer | 2020-09-24 | Update of analysis |
| html | dae157b | Philipp Bayer | 2020-09-24 | Update of analysis |
Here I run GAPIT’s methods with all phenotypes and the NLR gene matrix.
#devtools::install_github("jiabowang/GAPIT3", dependencies=TRUE)
# warning: GAPIT3 depends on LDheatmap, which was removed from CRAN. Install using devtools::install_github("cran/LDheatmap")
library(GAPIT3)Warning: replacing previous import 'multtest::wapply' by 'gplots::wapply' when
loading 'GAPIT3'Get all phenotypes:
phenos <- list.files('./data/', pattern = '*txt')
# remove larger data
phenos <- phenos[!grepl('txt.gz', phenos)]Got 39 phenotype files. Annoyingly, some files have several columns, some have only two (ID + Phenotype).
I’ve written a Python script which transforms the NLR gene PAV matrix into the format GAPIT wants (check code/transformToGAPIT.py).
OK let’s run GAPIT with the Python output.
myGD <- read.table('./data/NLR_PAV_GD.txt', head=TRUE)
myGM <- read.table('./data/NLR_PAV_GM.txt', head=TRUE)
#myKI <- read.table('./data/SNP_KI.txt', head=FALSE) # this was calculated using SNPs from
# https://research-repository.uwa.edu.au/files/89232545/SNPs_lee.id.biallic_maf_0.05_geno_0.1.vcf.gzI used MVP for that on Pawsey’s Zeus, the following code was run before remotely:
library(rMVP)
MVP.Data(fileVCF="SNPs_lee.id.biallic_maf_0.05_geno_0.1.vcf",
fileKin=FALSE,
filePC=FALSE,
out="mvp.vcf")
MVP.Data.Kin(TRUE, mvp_prefix='mvp.vcf', out='mvp')
MVP.Data.PC(TRUE, mvp_prefix='mvp.vcf', out='mvp', perc=1, pcs.keep=5)Then I need to fix the kinship matrix because the GAPIT format is a bit different, and the order needs to be identical.
Let’s run GAPIT then, this might take a few minutes:
for( i in seq_along(phenos)){
thisy <- phenos[i]
myY <- read.table(paste('data/', thisy, sep=''), head=TRUE)
# for now, let's skip those multicolumn phenotypes, I'm not sure what they are
if(ncol(myY) != 2) {
next
}
GAPIT(Y=myY[,c(1,2)],
GD=myGD,
GM=myGM,
model=c('GLM','MLM','FarmCPU'),
KI=myKI,
PCA.total = 0) # avoid calculating PCs based on PAV data
break
}
# gapit always seems to write to the current working directory. That annoys me.
# setwd() probably breaks something in workflowr,
# so let's just move the files all over
gapit_out <- list.files('.', pattern='GAPIT*')
for (i in seq_along(gapit_out)) {
thisf <- gapit_out[i]
# there's no file.move for some reason?!?
file.copy(from = thisf,
to = paste('output/GAPIT/', thisf, sep=''))
file.remove(thisf)
}
sessionInfo()R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)
Matrix products: default
locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
[5] LC_TIME=English_Australia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] GAPIT3_3.1.0 workflowr_1.6.2.9000
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 pillar_1.4.4 compiler_3.6.3
[4] later_1.1.0.1 git2r_0.27.1 bitops_1.0-6
[7] tools_3.6.3 getPass_0.2-2 digest_0.6.25
[10] lattice_0.20-41 evaluate_0.14 lifecycle_0.2.0
[13] tibble_3.0.2 pkgconfig_2.0.3 rlang_0.4.7
[16] Matrix_1.2-18 rstudioapi_0.11 yaml_2.2.1
[19] parallel_3.6.3 xfun_0.17 httr_1.4.2
[22] stringr_1.4.0 knitr_1.29 caTools_1.18.0
[25] gtools_3.8.1 fs_1.5.0.9000 vctrs_0.3.1
[28] stats4_3.6.3 grid_3.6.3 rprojroot_1.3-2
[31] multtest_2.42.0 Biobase_2.46.0 glue_1.4.2
[34] R6_2.4.1 processx_3.4.4 survival_3.2-3
[37] rmarkdown_2.3 gdata_2.18.0 callr_3.4.4
[40] magrittr_1.5 whisker_0.4 gplots_3.0.3
[43] MASS_7.3-51.6 splines_3.6.3 backports_1.1.10
[46] ps_1.3.4 promises_1.1.1 ellipsis_0.3.1
[49] htmltools_0.5.0 BiocGenerics_0.32.0 httpuv_1.5.4
[52] KernSmooth_2.23-17 stringi_1.5.3 crayon_1.3.4