read.mbias: Read the M-bias.txt file produced from Bismark.

In PeteHaitch/cometh: Analyse, manage and visualise co-methylation data.

Description

Read the M-bias.txt file produced from Bismark and return as a data.frame.

Usage

read.mbias(file)

Arguments

file	The name of the M-bias file which the data are to be read from.

Value

A data.frame. The columns are:

• read: SE if the data are from single-end sequencing; R1 or R2 if the data are read_1 or read_2 from paired-end sequencing.

• read_pos: the position along the read.

• methylation_type: the methylation type. Either "CG", "CHG", "CHH".

• M: the number of methylated base calls.

• U: the number of unmethylated base calls.

• total: the total number of base calls.

• perc_M: the percentage of methylated base calls.

Note

WARNING: The "position along the read" is only the same as the "sequencing cycle" if the reads did not undergo any pre-alignment trimming.

Examples

cat("TODO")

PeteHaitch/cometh documentation built on May 8, 2019, 1:32 a.m.