compare_samples: Complete Methylation Analysis of Next Generation Sequencing...

In MethTargetedNGS: Perform Methylation Analysis on Next Generation Sequencing Data

Description

This function perform complete methylation analysis of the data.

1. Visualize methylation pattern

2. Calculate methylation average

3. Calculate methylation entropy

4. Perform fisher exact test on the samples to identify significant CpG sites.

Usage

compare_samples(healthy, tumor)

Arguments

healthy	: Output Matrix from methAlign
tumor	: Output Matrix from methAlign

Value

Generate a plot of Methylation Average, Methylation Entropy, Fisher Exact Test and Log Odd Ratio

Note

This function needs time to process depending on the number of sequences in fasta file

Author(s)

Muhammad Ahmer Jamil, Prof. Holger Frohlich, Priv.-Doz. Dr. Osman El-Maarri

Maintainer: Muhammad Ahmer Jamil [e-mail]

See Also

methAlign, methAvg, methEntropy, odd_ratio, fishertest_cpg,

Examples

healthy = system.file("extdata", "Healthy.fasta", package = "MethTargetedNGS")
tumor = system.file("extdata", "Tumor.fasta", package = "MethTargetedNGS")
reference =  system.file("extdata", "Reference.fasta", package = "MethTargetedNGS")

healthy = methAlign(healthy,reference)
tumor = methAlign(tumor,reference)
compare_samples(healthy,tumor)

Example output

Loading required package: stringr
Loading required package: seqinr
Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

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:gplots':

    space

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:seqinr':

    translate

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

    strsplit

Time difference of 1.93 secs
Time difference of 1.38 secs
Time difference of 0.01 secs
Time difference of 0.01 secs

MethTargetedNGS documentation built on Nov. 8, 2020, 8:10 p.m.