Hi, I was trying to analyze my RNA seq data with Deseq2. Now I have finished mapping step with HISAT2, generated a count matrix as input for Deseq2, from the manual of StringTie, I know that I should use "DESeqDataSetFromMatrix" to read. but how to use it, I am not sure. in the manual of Deseq2, it gave an example of how to read in the count matrix in a R package as follows:
library("pasilla")
pasCts <- system.file("extdata", "pasilla_gene_counts.tsv",
package="pasilla", mustWork=TRUE)
pasAnno <- system.file("extdata", "pasilla_sample_annotation.csv",
package="pasilla", mustWork=TRUE)
countData <- as.matrix(read.csv(pasCts,sep="\t",row.names="gene_id"))
colData <- read.csv(pasAnno, row.names=1)
colData <- colData[,c("condition","type")]
but I just to directly read "transcript_count_matrix.csv" in my current directory, How could I achieve that?
Thanks!
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Wet&DryImmunology
countData = read.csv("transcript_count_matrix.csv")
or some variant of it.
TKS! Devon.
looking at:
countData <- as.matrix(read.csv(pasCts,sep="\t",row.names="gene_id"))
I was imaging something much more complicated than you suggested.
Indeed. Could someone familiar with DEseq2 clarify this. Going to try, but I am guessing just countData = read.csv("transcript_count_matrix.csv") is not going to work.
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