methEntropy: Calculate Methylation Entropy

In MethTargetedNGS: Perform Methylation Analysis on Next Generation Sequencing Data

Description

Entropy comparison between healthy and tumor samples can identify significant CpG sites which are contributing most in the tumor development either by hypomethylation or hypermethylation. Also such way can help in understanding the randomness in methylation status. Sliding window of 4 was used to calculate the entropy in the sample, which can analyze 16 different pattern for entropy calculation.

Usage

methEntropy(x)

Arguments

x	Matrix from methAlign. Also matrix where columns represents Cytosine of CpG sites and rows represents sequences

Value

Matrix containing entropy for every sequence and group of 4 cpg sites.

Note

This function needs time to process depending on the number of rows in matrix

Author(s)

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

Maintainer: Muhammad Ahmer Jamil [e-mail]

References

Xie, H., Wang, M., de Andrade, A., Bonaldo, M.d.F., Galat, V., Arndt, K., Rajaram, V., Goldman, S., Tomita, T. and Soares, M.B. (2011) Genome-wide quantitative assessment of variation in DNA methylation patterns. Nucleic Acids Research, 39, 4099-4108.

See Also

methAlign

Examples

healthy = system.file("extdata", "Healthy.fasta", package = "MethTargetedNGS")
reference = system.file("extdata", "Reference.fasta", package = "MethTargetedNGS")
methP <- methAlign(healthy,reference)
entMeth <- methEntropy(methP)
plot(entMeth,type="l")

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, cbind, colMeans, colSums, colnames, 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 2.03 secs
Time difference of 0.02 secs

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