read.BisXP {BisRNA}

Read RNA bisulfite experiment data and cast it into a BisXP object

Description

read.BisXP reads a table containing RNA name, C position, bisulfite non-conversion ratio and adjusted p-value from a file and casts it into a BisXP object.

Usage

read.BisXP(filename)

Arguments

filename

Address of the file containing data from a bisulfite experiment in 4 columns separated by a tabulation, with header on the first line:

• RNA name

• C position (integer, in [1,+Inf])

• bisulfite non-conversion ratio (numeric, in [0,1])

• pvalue.adj (numeric, in [0,1])

Details

This function takes a file name as input, reads the bisulfite data table contained in this file, performs checks, and casts the data into a BisXP object, which contain input data with rows labelled after a RNA_C.position pattern.

Value

If the input table is correct, then the output will be a BisXP object corresponding to a consolidated data frame with rows labelled after a RNA_C.position pattern.

Examples

 RNAs     <- c("NM_00001","NM_00001","NM_00002")
 Cpos     <- c(1,5,1)
 ncratio  <- c(0.1,0.5,0.3)
 pv.adj   <- c(0.001,0.1,0.3)
 BSdata <- data.frame(RNAs, Cpos, ncratio, pv.adj)