read_profile {seqCAT} | R Documentation |
Read SNV profiles for use in downstream comparisons.
read_profile(file, sample_name, remove_mt = TRUE)
file |
The SNV profile to be read (path). |
sample_name |
The sample of the SNV profile (character). |
remove_mt |
Remove or keep mitochondrial variants (boolean). |
This is a function for reading SNV profiles created from VCF files. The data is returned as a GenomicRanges object, suitable for merging of metadata.
A GRanges object.
# Path to test data profile = system.file("extdata", "test_profile_1.txt.gz", package = "seqCAT") # Read test profile profile_1 <- read_profile(profile, "sample1")