cgInAlign: Amount of CpGs

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

Description

Calculating amount of CpGs between alignments border

Usage

cgInAlign(methData)

Arguments

methData

An object of type list that contains information on the pairwise alignments and methylation status of all CpG motifs under study. Created by applying MethAlignNW()

Details

This function computes the amount of CpGs on the positions corresponds to genomic sequence over all sequences under study between the alignment borders.

Value

Integer vector of CpG amount

Author(s)

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

Examples

data(methData)
cgInAlign(methData)

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