Cytofile_read: Read the cyto file.

In xiaowangCN/GeneDMRs: GeneDMRs: an R package for Gene-based differentially methylated regions analysis

Read the cyto file.

Description

This function reads the chromosome information from cyto file (cytoBandIdeo.txt) and sort them by chromosome and position. The dataset of the example is the mouse genome information downloaded from UCSC website (http://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/cytoBandIdeo.txt.gz).

Usage

Cytofile_read(
  paths = paste(system.file(package = "GeneDMRs"), "/methdata", sep = ""),
  cytofile = "cytoBandIdeo",
  suffix = ".txt.gz"
)

Arguments

paths	refers to the path of input file, with default the package path.
cytofile	refers to the name of input cyto file that is downloaded from UCSC website, with default "cytoBandIdeo".
suffix	refers to the suffix of input cyto file, e.g., ".gz", ".zip" and so on (some files are in text .txt format, then ".txt" or ".txt.gz"), with default ".txt.gz".

Value

Outputs a data frame contains chromosome, start position, end position.

Examples

inputcytofile <- Cytofile_read()
inputcytofile <- Cytofile_read(paths = paste(system.file(package = "GeneDMRs"), "/methdata", sep=""),
cytofile = "cytoBandIdeo", suffix = ".txt.gz")

xiaowangCN/GeneDMRs documentation built on Nov. 22, 2023, 11:19 p.m.