RPKM_calc: RPKM calculation for the genomic features

In stiv1n/CYCLeR: CircRNA transcriptome assembly tool

RPKM calculation for the genomic features

Description

RPKM calculation for the genomic features

Usage

RPKM_calc(
  count_matrix,
  sg,
  bsj_granges,
  bs_genome,
  sample_table,
  feature_type,
  fsj_overhang = 3,
  bsj_overhang = 15,
  eff_length_correction = T,
  gc_correction = F
)

Arguments

count_matrix	count matrix corresponding to the features
sg	SGSeq object supplying feature info
bsj_granges	GRange of BSJ cooredinates
bs_genome	a BSGenome object used for extracting the sequences
sample_table	sample table formatted according to the manual, Must contain “sample_name” “treatment” “file_bam” “lib_size” “read_len”; NB the values in column “treatment” can only be “control” and “enriched”
feature_type	either “e” for exons ot “j” for junctions
fsj_overhang	the FJS overhand used in the mapping a.k.a. anchor
bsj_overhang	the BSJ overhand used in the chimeric detection
eff_length_correction	whether or not to apply effective length correction
gc_correction	whether or not to apply GC-content correction; requires further testing

Details

This function performs RPKM calculations for the exonic features. The RPKM calculation is performed based on the exact sequences for the exons. For junctions, the sequences are selected based on the exons, flanking the junction. The function takes into account the needed effective length corrections.

Value

BAMFileList object with info on the trimmed files

Author(s)

Stefan Stefanov

stiv1n/CYCLeR documentation built on Sept. 15, 2022, 4:39 p.m.