chromReads: chromReads

In amitjavilaventura/seqViewR: Visualization of Omics And Sequencing Data In R

chromReads

Description

Function counts the reads mapped to each chromosome and plots a bar graph. It uses the function idxstatsBam() from the Rsamtools R package. Run help("idxstatsBam") for more information.

Usage

chromReads(bamfile, bamindex = NULL, chr.filt = "", main = NULL, main.size = 13, subtitle = NULL, sub.size = 11, xlab = "Mapped reads", ylab = "Chromosome", axis.size = 9, percent.label = T, percent.size = 3)

Arguments

bamfile	Character of lenght 1. Path to the BAM file whose reads are to be mapped.
bamindex	Character of length 1 or NULL. Path to the index of the BAM file in 'bamfile'. If null, it will search a file with the same base name as the 'bamfile' and extension '.bam.bai'. Default: NULL
chr.filt	Character. Vector of undefined length with strings to filter chromosomes (i.e. "Un" would filter all chromosomes containing "Un" in their name). Default: c("Un", "random", "GL", "JH", "\*").
main	Character of lenght 1. Title of the plot. Default: NULL.
main.size	Numeric of length 1. Font size of the title. It works only if main is not NULL. Default: 13.
subtitle	Character of lenght 1. Subtitle of the bar plot. It works only if main is not NULL. Default: NULL.
sub.size	Numeric of length 1. Font size of the subtitle. It works only if main is not NULL. Default: 11.
xlab	Character of lenght 1. Title of the X axis. Default: "Mapped reads".
ylab	Character of lenght 1. Title of the Y axis. Default: "Chromosome".
axis.size	Numeric of length 1. Size of the axis labels. Default: 9
percent.label	Logical of lenght 1. If TRUE, it draws the percentage of reads in each chromosome.
percent.size	Character of lenght 1. Size of the percentage drawn in the plot.

Author(s)

amitjavilaventura

amitjavilaventura/seqViewR documentation built on Nov. 21, 2023, 10:12 a.m.