read.BisXP {BisRNA}R Documentation

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


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.





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])


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.


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.


 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)

[Package BisRNA version 0.2.2 Index]