makeDataMethGFF: GFF methylation files

In methVisual: Methods for visualization and statistics on DNA methylation data

Description

Create methData object from processed .gff files

Usage

makeDataMethGFF(dir,chr,start,end,meth_value)

Arguments

dir	String; The local directory where the .gff files are located
chr	String; Chromosome under study
start	Integer; The start position of genomic region under study
end	Integer; The end position of the genomic region under study
meth_value	double; level of methylation on CpG

Details

This function reads and processes GFF files and creates a list object (like the one generated by MethAlignNW()) which can be later analyzed through the visualization, classification and clustering functions.

Value

methData object

Author(s)

Arie Zackay <[e-mail]>, Christine Steinhoff <[e-mail]>

Examples

methGFF <- makeDataMethGFF(dir=system.file(package="methVisual",
			"examples/GFF"),chr="7",start=0,end=70,0.75)
methGFF

Example output

Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: plotrix
Loading required package: gsubfn
Loading required package: proto
Loading required package: grid
Loading required package: sqldf
Loading required package: RSQLite
Warning message:
no DISPLAY variable so Tk is not available 
processing  1.gff 
processing  1.gff  DONE 
extracting data from  1.gff  DONE 
processing  2.gff 
processing  2.gff  DONE 
extracting data from  2.gff  DONE 
processing  3.gff 
processing  3.gff  DONE 
extracting data from  3.gff  DONE 
processing  4.gff 
processing  4.gff  DONE 
extracting data from  4.gff  DONE 
processing  5.gff 
processing  5.gff  DONE 
extracting data from  5.gff  DONE 
$seqName
[1] "1.gff" "2.gff" "3.gff" "4.gff" "5.gff"

$methPos
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
[1,]    1    1    0    0    1    0    0    0
[2,]    1    1    0    0    1    0    0    2
[3,]    1    1    0    1    1    0    1    2
[4,]    1    1    0    1    1    0    1    0
[5,]    1    1    1    1    1    1    1    1

$positionCGIRef
[1]  2 10 15 22 32 40 60 64

$startEnd
     [,1] [,2]
[1,]    2   64
[2,]    2   60
[3,]    2   60
[4,]    2   64
[5,]    2   64

$lengthRef
[1] 72

methVisual documentation built on April 28, 2020, 7:08 p.m.