getSGFeatureCounts {SGSeq} | R Documentation |
Compatible counts are obtained for each sample and combined into
an SGFeatureCounts
object.
getSGFeatureCounts(sample_info, features, min_anchor = 1, counts_only = FALSE, verbose = FALSE, cores = 1)
sample_info |
Data frame with sample information.
Required columns are “sample_name”, “file_bam”,
“paired_end”, “read_length”, “frag_length”
and “lib_size”. Library information can be obtained with
function |
features |
|
min_anchor |
Integer specifiying minimum anchor length |
counts_only |
Logical indicating only counts should be returned |
verbose |
If |
cores |
Number of cores available for parallel processing |
codeSGFeatureCounts object, or integer matrix of counts
if counts_only = TRUE
Leonard Goldstein
path <- system.file("extdata", package = "SGSeq") si$file_bam <- file.path(path, "bams", si$file_bam) sgfc <- getSGFeatureCounts(si, sgf_pred)