I am referring to an R code available on https://rdrr.io/bioc/ATACseqQC/man/TSSEscore.html where reading the file is suggested as:
bamfile <- system.file("extdata", "GL1.bam",
package="ATACseqQC", mustWork=TRUE)
When I am trying to do this on my file as below it gives me an error
bamfile <- system.file("extdata", "RRrep1_rmDupChrC_sorted.bam", package="ATACseqQC", mustWork=TRUE)
Error in system.file("extdata", "RRrep1_rmDupChrC_sorted.bam", package = "ATACseqQC", :
no file found
list.files()
[1] "RRrep1_rmDupChrC_sorted.bam"
Please help me to understand why system.file function does not allow to read my file.