makeBSseqData: Create an object of BSseq class from several data frames.

In DSS: Dispersion shrinkage for sequencing data

Description

This is an utility function to merge BS-seq data from replicated experiment and create an object of BSseq class.

After sequence alignment and proper processing, the BS-seq data can be summarized by following information at each C position (mostly CpG sites, with some CH): chromosome number, genomic coordinate, total number of reads covering the position, and number of reads showing methylation at this position. For replicated samples, the data need to be merged based on the chromosome number and genomic coordinates. This function provide such functionality. It takes replicated data as a list of data frames, merged them, and create a BSseq object.

Usage

makeBSseqData(dat, sampleNames)

Arguments

dat	A list of multiple data frames from biological replicates. Each element represents data from one replicate. The data frame MUST contain following columns in correct order: (1) Chromosome number; (2) Genomic coordinates; (3) Read coverage of the position from BS-seq data; (4) Number of reads showing methylation of the position. The colnames MUST BE "chr", "pos", "N", "X".
sampleNames	A vector of characters for the sample names. The length of the vector should match the length of the input list.

Value

An object of 'BSseq' class.

Author(s)

Hao Wu <[e-mail]>

See Also

callDML

Examples

require(bsseq)

## first read in methylation data.
path <- file.path(system.file(package="DSS"), "extdata")
dat1.1 <- read.table(file.path(path, "cond1_1.txt"), header=TRUE)
dat1.2 <- read.table(file.path(path, "cond1_2.txt"), header=TRUE)
dat2.1 <- read.table(file.path(path, "cond2_1.txt"), header=TRUE)
dat2.2 <- read.table(file.path(path, "cond2_2.txt"), header=TRUE)

## make BSseq objects
BSobj <- makeBSseqData( list(dat1.1, dat1.2, dat2.1, dat2.2),
  c("C1","C2", "N1", "N2") )

BSobj
sampleNames(BSobj)

Example output

Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: bsseq
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    apply

Loading required package: splines
An object of type 'BSseq' with
  34739 methylation loci
  4 samples
has not been smoothed
All assays are in-memory
[1] "C1" "C2" "N1" "N2"
Warning message:
system call failed: Cannot allocate memory 

DSS documentation built on Nov. 8, 2020, 7:44 p.m.