splitDataByGRanges: Split methylation data into regions based on the genomic...

View source: R/utils.R

splitDataByGRangesR Documentation

Split methylation data into regions based on the genomic annotations

Description

This function splits the methylation data into regions based on the genomic annotations provided under the form of a GenomicRanges object.

Usage

splitDataByGRanges(
  dat,
  chr,
  annots,
  gap = -1,
  min.cpgs = 50,
  max.cpgs = 2000,
  verbose = TRUE
)

Arguments

dat

a data frame with rows as individual CpGs appearing in all the samples. The first 4 columns should contain the information of Meth_Counts (methylated counts), Total_Counts (read depths), Position (Genomic position for the CpG site) and ID (sample ID). The covariate information, such as disease status or cell type composition, are listed in column 5 and onwards.

chr

character vector containing the chromosome information. Its length should be equal to the number of rows in dat.

annots

GenomicRanges object containing the annotations

gap

integer defining the maximum gap that is allowed between two regions to be considered as overlapping. According to the GenomicRanges::findOverlaps function, the gap between 2 ranges is the number of positions that separate them. The gap between 2 adjacent ranges is 0. By convention when one range has its start or end strictly inside the other (i.e. non-disjoint ranges), the gap is considered to be -1. Decimal values will be rounded to the nearest integer. The default value is -1 (meaning strict overlaping).

min.cpgs

positive integer defining the minimum number of CpGs within a region for the algorithm to perform optimally. The default value is 50.

max.cpgs

positive integer defining the maximum number of CpGs within a region for the algorithm to perform optimally. The default value is 2000.

verbose

logical indicates if the algorithm should provide progress report information. The default value is TRUE.

Value

A named list of data.frame containing the data of each independent region.

Author(s)

Audrey Lema├žon

Examples

#------------------------------------------------------------#
data(RAdat)
RAdat.f <- na.omit(RAdat[RAdat$Total_Counts != 0, ])
annot <- GenomicRanges::GRanges(seqnames = "chr1", IRanges::IRanges(
start = c(102711720,102711844,102712006,102712503,102712702), 
end = c(102711757,102711909,102712195,102712637,102712712)
))
results <- splitDataByGRanges(dat = RAdat.f, 
chr = rep(x = "chr1", times = nrow(RAdat.f)), 
annots = annot, gap = -1, min.cpgs = 5)

kaiqiong/SOMNiBUS documentation built on June 3, 2022, 9:16 a.m.