I ran the **combat-seq** for my data
The full program was executed, but its output is as follows
I checked the code several times and I do not know where the problem is
Can you help?
files <-list.files(“.”,”*.count”)
cnt <- lapply(files,read.delim,header=F)
cnt<- lapply(files,read.delim,header=F,stringsAsFactors=F)
cnt<-do.call(cbind,cnt)
cnt<- cnt[,-seq(1,ncol(cnt),2)]
colnames(cnt)<- sub(“.count”,””,files)
batch<- samplerace
samplecondition <- factor(rep(c(‘control’,’control’,’fibrosis’,’fibrosis’),84))
covariate_matrix = cbind(group,samplegender)
cntcombat<-ComBat_seq(cnt,batch= batch,full_mod=TRUE,group=NULL,
covar_mod = covariate_matrix)
head(cntcombat)
[[1]]
[1] 50
[[2]]
[1] 11
[[3]]
[1] 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[70] 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[139] 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[208] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
[277] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 …
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