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  • salmon tximport file vector question

    Sorry for the noob question which is probably due to my poor understanding of R... Salmon generates a folder with the sample name for each sample, with inside it, a quant.sf file. Can someone give me a concrete example of how I define the files in the tximport statement. The sample code below from Mike Love doesn't help me, as it seems to have toy names.

    files <- file.path(dir, "salmon", samples$run, "quant.sf")
    names(files) <- paste0("sample", 1:6)
    txi.salmon <- tximport(files, type = "salmon", tx2gene = tx2gene, reader = read_tsv)

    Thanks in advance

  • #2
    Hi humphreyg,

    Those commands are building up a 'named vector' of the location of each file. You could manually give it the location of each file like so:

    files <- c("salmon/sample1/quant.sf", "salmon/sample2/quant.sf", "salmon/sample3/quant.sf")

    names(files) <- c("sample1", "sample2", "sample3")

    You'll need to replace "sample1", etc., with the actual names and locations of your files.

    Best,

    Matt.

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