MEDME.writeFiles: writeFiles sgr or gff files from MEDME output

In MEDME: Modelling Experimental Data from MeDIP Enrichment

Description

allows to write sgr or gff files after MEDME analysis

Usage

MEDME.writeFiles(data, output, path = getwd(), format, featureLength  = NULL)

Arguments

data	An object of class MEDMEset
output	string; the name of the data slot to be written on the disk, either logR, smoothed, AMS or RMS
path	string; the path where the files are stored; the current working directory is the default
format	string; either sgr or gff to indicate the respective file formats
featureLength	integer; in case of GFF file format the length of the features has to be provided to determine start and end positions

Details

One GFF or SGR file is provided for each sample of the data MEDMEset object.

In case of GFF files, tab-delimited files with header are provided with following fields for each probe: chromosome, empty field, probe ids, start and stop chromosomal positions, and score and empty fields.

In case of sgr files, tab-delimited files with no header and chr, chr positions and score are provided.

MEDME documentation built on Nov. 8, 2020, 5:31 p.m.