SGSeq (version 1.6.5)

getSGFeatureCounts: Compatible counts for splice graph features from BAM files

Description

Compatible counts are obtained for each sample and combined into an SGFeatureCounts object.

Usage

getSGFeatureCounts(sample_info, features, min_anchor = 1, counts_only = FALSE, verbose = FALSE, cores = 1)

Arguments

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 getBamInfo.

features

SGFeatures object

min_anchor

Integer specifiying minimum anchor length

counts_only

Logical indicating only counts should be returned

verbose

If TRUE, generate messages indicating progress

cores

Number of cores available for parallel processing

Value

codeSGFeatureCounts object, or integer matrix of counts if counts_only = TRUE

Examples

path <- system.file("extdata", package = "SGSeq")
si$file_bam <- file.path(path, "bams", si$file_bam)
sgfc <- getSGFeatureCounts(si, sgf_pred)