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I am not very familiar with loops in R, and am having a hard time stating a variable such that it is recognized by a function, DESeqDataSetFromMatrix.

pls is a table of integers. metaData is a data frame containing sample IDs and conditions corresponding to pls. I verified that the below steps run error-free with the individual elements of cond run successfully .

I reviewed relevant posts on referencing variables in R: How to reference variable names in a for loop in R? How to reference a variable in a for loop?

Based on these posts, I modified i in line 3 with single brackets, double brackets and "as.name". No luck. DESeqDataSetFromMatrix is reading the literal text after ~ and spits out an error.

cond=c("wt","dhx","mpp","taz")
for(i in cond){
dds <- DESeqDataSetFromMatrix(countData=pls,colData=metaData,design=~i, tidy = TRUE)
"sizeFactors"(dds) <- 1
paste0("PLS",i)<-DESeq(dds)
pdf <- paste(i,"-PLS_MA.pdf",sep="")
tsv <- paste(i,"-PLS.tsv",sep="")
pdf(file=pdf,paper = "a4r", width = 0, height = 0)
plotMA(paste0("PLS",i),ylim=c(-10,10))
dev.off()
write.table(results(paste0("PLS",i)),file = tsv,quote=FALSE, sep='\t', col.names = NA)
}

With brackets, an unexpected symbol error populates. With i alone, DESEqDataSetFromMatrix tries to read "i" from my metaData column.

Is R just not capable of reading variables in some situations? Generally speaking, is it better to write loops outside of R in a more straightforward language, then push as standalone commands? Thanks for the help—I hope there is an easy fix.

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1 Answers1

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For anyone else who may be having trouble looping with DESeq2 functions, comments above addressed my issue.

Correct input:

dds <- DESeqDataSetFromMatrix(countData=pls,colData=metaData,design=as.formula(paste0("~", i)), tidy = TRUE)

as.formula worked well with all DESeq functions that I tested.

reformulate(i) also worked well in most situations.

Thanks, everyone for the help!

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