plotCoverageOverLocus: plot coverage over locus

Description Usage Arguments

View source: R/BamFunctions.R

Description

ggbio plot with transcripts track and coverage track

Usage

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plotCoverageOverLocus(
  bamfile_path,
  annote_db,
  gene_id,
  strandedness,
  quality_threshold = 20L
)

Arguments

bamfile_path

path to a bam file

annote_db

a GenomicFeatures TxDb object. Maybe one made from a gtf, eg txdb = makeTxDbFromGFF("data/liftoff_h99_to_kn99.gtf", format = "gtf")

gene_id

a gene_id of interest – must be in the gene names of the annote_db object

strandedness

one of c("reverse", "unstranded"). NOTE: forward only strand NOT currently configured

quality_threshold

quality threshold above which reads will be considered. 20l is default, which is chosen b/c it is the default for HTSeq


cmatKhan/brentlabRnaSeqTools documentation built on Nov. 17, 2021, 5:47 a.m.