SGSeq (version 1.6.5)

getSGVariantCounts: Representative counts and frequency estimates for splice variants

Description

For splice variants, obtain counts of compatible fragments spanning the start and/or end of each variant. Counts can be obtained from an SGFeatureCounts object or from BAM files. Only one of the two arguments feature_counts or sample_info must be specified. Local estimates of relative usage are calculated at the start and/or end of each splice variant. For splice variants with relative usage estimates at both start and end, these are combined by taking a weighted mean, where weights are proportional to the total number of reads spanning the respective boundary.

Usage

getSGVariantCounts(variants, feature_counts = NULL, sample_info = NULL, min_denominator = NA, min_anchor = 1, verbose = FALSE, cores = 1)

Arguments

variants

SGVariants object

feature_counts

SGFeatureCounts object

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.

min_denominator

Integer specifying minimum denominator when calculating variant frequencies. The total number of boundary-spanning reads must be equal to or greater than min_denominator for at least one event boundary. Otherwise estimates are set to NA. If NA, all estimates are returned.

min_anchor

Integer specifiying minimum anchor length

verbose

If TRUE, generate messages indicating progress

cores

Number of cores available for parallel processing

Value

SGVariantCounts object

Examples

sgvc_from_sgfc <- getSGVariantCounts(sgv_pred, sgfc_pred)
path <- system.file("extdata", package = "SGSeq")
si$file_bam <- file.path(path, "bams", si$file_bam)
sgvc_from_bam <- getSGVariantCounts(sgv_pred, sample_info = si)