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?