I am trying to read the results in files called 'SRR11834853' and similar names with different numbers. I am using this script:

ppolSampleInfo = read.table("./RNAseq2/Workplace/1_raw/metadata2.txt",header=TRUE, fill = TRUE)

row.names(ppolSampleInfo) <- ppolSampleInfo$sampleName

head(ppolSampleInfo)

ddsHTSeq<-DESeqDataSetFromHTSeqCount(sampleTable= ppolSampleInfo, directory = "~/RNASeq2/Workplace/4_counts", design = ~ condition)

dds<-DESeq(ddsHTSeq)

and when I run the second last line it gives:

Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'Users/RNASeq2/Workplace/4_counts/male_adult_eyes': No such file or directory

The problem is that its looking for files (in the right place) with names from the wrong column of my metadata file, it should be looking at the column labelled 'sampleName', but it looks like it's looking at the column labelled 'fileName'

How do I change this?

With R functions you can always consult

?functionName

it describes the arguments and how they are used:

for htseq-count: a data.frame with three or more columns. Each row describes one sample. The first column is the sample name, the second column the file name of the count file generated by htseq-count, and the remaining columns are sample metadata which will be stored in colData