how arrange samples columns according to row names from another file in R
1
0
Entering edit mode
4 months ago
Bioinfonext ▴ 460

Hi all,

Could you please let me know how we can arrange mval columns in same order as targets2 row names.

#phenotype file
targets<-read.table("limma.phenos.hba1c.304.txt", header=TRUE, stringsAsFactor=FALSE,row.names=NULL, sep="\t")



head(targets2)
                  BeadChipID sex age creat_umol_per_L    creat      eGFR Batch
DC464   202995740113_R06C01   1  30               85 0.961520 108.84266     8
DDN89   200788250048_R07C01   1  51               80 0.904960 102.72419     6
DC223   200788250033_R04C01   0  41               59 0.667408 112.64654     6
dim(targets2)
[1] 304  21
#read mehtylation data

###################





mval <- read.table("beta.new.304.csv",sep=",", as.is=T, na.strings="NA", check.names=FALSE, header =T)





 head(mval, 10) [,1:5]
                  DN54      DC146      DDN44      DC179      DN121
    cg26928153  2.4791678  2.8599419  2.7693438  3.1229033  2.9644520
    cg16269199  1.4452663  1.4528645  1.6557921  1.7818135  1.9590533
    cg13869341  2.4145157  2.6571868  2.1751019  3.1139991  3.4626554
statistics r biostatistics • 262 views
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1
Entering edit mode
4 months ago

This isn't really a bioinformatics question, but you can do:

mval <- mval[, rownames(targets2)]
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