getMappingRatesFromPairs: To get mapping rates in all pairs of haplotypes and produce...

In jknightlab/AltHapAlignR: AltHapAlignR: Haplotype-specific mapping in RNA-seq

Description

To get mapping rates in all pairs of haplotypes and produce summerized figure

Usage

getMappingRatesFromPairs(ed_table, hap_names = c("apd", "cox", "dbb", "mann",
  "mcf", "pgf", "qbl", "ssto"), read_length = 50)

Arguments

ed_table	a file with a table of editing distances generated from a function 'EDframBams'
hap_names	haplotype names matching to column names of the input file 'ed_table' (eg. c("apd", "cox", "dbb", "mann", "mcf", "pgf", "qbl", "ssto") )
read_length	read length in bam files

Examples

ed_table=system.file("extdata", "example_ed_table.txt", package = "AltHapAlignR")
ed_table <- read.table(ed_table, sep="\t", header=TRUE)
output <- getMappingRatesFromPairs(ed_table, 
               hap_names=c("apd", "cox", "dbb", "mann", "mcf", "pgf", "qbl", "ssto"), 
               read_length=50)

jknightlab/AltHapAlignR documentation built on Sept. 11, 2019, 9:02 p.m.