SGSeq (version 1.2.2)

getSGVariantCounts: Representative counts and frequency estimates for splice variants

Description

For splice variants obtain counts of compatible fragments extending across the start or end of each variant. Counts can be obtained from an SGFeatureCounts object or from BAM files. Only one of the two arguments object and sample_info must be specified. Splice variant frequencies are estimated based on representive counts.

Usage

getSGVariantCounts(variants, object = NULL, features = NULL, sample_info = NULL, verbose = FALSE, cores = 1)

Arguments

variants

SGVariants object

object

SGFeatureCounts object

features

SGFeatures object that must include all features included in featureID5p(variants) and featureID3p(variants)

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.

verbose

If TRUE, generate messages indicating progress

cores

Number of cores available for parallel processing

Value

An SGVariantCounts object

Examples

sgvc_from_sgfc <- getSGVariantCounts(sgv, sgfc)
path <- system.file("extdata", package = "SGSeq")
si$file_bam <- file.path(path, "bams", si$file_bam)
sgvc_from_bam <- getSGVariantCounts(sgv, features = sgf, sample_info = si)