getSGFeatureCounts {SGSeq} | R Documentation

## 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`

### 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)

[Package SGSeq version 1.16.2 Index]