getSGFeatureCounts: Compatible counts for splice graph features from BAM files

In ldg21/SGSeq: Splice event prediction and quantification from RNA-seq data

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

Author(s)

Leonard Goldstein

Examples

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

ldg21/SGSeq documentation built on Oct. 14, 2020, 9:51 p.m.