constructBins {mosaics} | R Documentation

## Construct bin-level ChIP-sep data from an aligned read file

### Description

Preprocess and construct bin-level ChIP-sep data from an aligned read file.

### Usage

    constructBins( infile=NULL, fileFormat=NULL, outfileLoc="./",
        byChr=FALSE, useChrfile=FALSE, chrfile=NULL, excludeChr=NULL,
        PET=FALSE, fragLen=200, binSize=200, capping=0, perl = "perl" )

### Arguments

`infile` | Name of the aligned read file to be processed.
`fileFormat` | Format of the aligned read file to be processed. Currently, `constructBins` permits the following aligned read file formats for SET data (`PET = FALSE`): `"eland_result"` (Eland result), `"eland_extended"` (Eland extended), `"eland_export"` (Eland export), `"bowtie"` (default Bowtie), `"sam"` (SAM), `"bam"` (BAM), `"bed"` (BED), and `"csem"` (CSEM). For PET data (`PET = TRUE`), the following aligned read file formats are allowed: `"eland_result"` (Eland result), `"sam"` (SAM), and `"bam"` (BAM).
`outfileLoc` | Directory of processed bin-level files. By default, processed bin-level files are exported to the current directory.
`byChr` | Construct separate bin-level file for each chromosome? Possible values are `TRUE` or `FALSE`. If `byChr=FALSE`, bin-level data for all chromosomes are exported to one file. If `byChr=TRUE`, bin-level data for each chromosome is exported to a separate file. Default is `FALSE`.
`useChrfile` | Is the file for chromosome info provided? Possible values are `TRUE` or `FALSE`. If `useChrfile=FALSE`, it is assumed that the file for chromosome info is not provided. If `useChrfile=TRUE`, it is assumed that the file for chromosome info is provided. Default is `FALSE`.
`chrfile` | Name of the file for chromosome info. In this file, the first and second columns are ID and size of each chromosome, respectively.
`excludeChr` | Vector of chromosomes that will be excluded from the analysis. This argument is ignored if `useChrfile=TRUE`.
`PET` | Is the file paired-end tag (PET) data? If `PET=FALSE`, it is assumed that the file is SET data. If `PET=TRUE`, it is assumed that the file is PET data. Default is `FALSE` (SET data).
`fragLen` | Average fragment length. Default is 200. This argument is ignored if `PET=TRUE`.
`binSize` | Size of bins. Default is 200.
`capping` | Maximum number of reads allowed to start at each nucleotide position. To avoid potential PCR amplification artifacts, the maximum number of reads that can start at a nucleotide position is capped at `capping`. Capping is not applied if non-positive value is used for `capping`. Default is 0 (no capping).
`perl` | Name of the perl executable to be called. Default is `"perl"`.

### Details

Bin-level files are constructed from the aligned read file and exported to the directory specified in `outfileLoc` argument. If `byChr=FALSE`, bin-level files are named as `[infileName]_fragL[fragLen]_bin[binSize].txt` for SET data (`PET = FALSE`) and `[infileName]_bin[binSize].txt` for PET data (`PET = TRUE`). If `byChr=TRUE`, bin-level files are named as `[infileName]_fragL[fragLen]_bin[binSize]_[chrID].txt`for SET data (`PET = FALSE`) and `[infileName]_bin[binSize]_[chrID].txt` for PET data (`PET = TRUE`), where `chrID` is chromosome IDs that reads align to. These chromosome IDs are extracted from the aligned read file.

If the file for chromosome information is provided (`useChrfile=TRUE` and `chrfile` is not NULL), only the chromosomes specified in the file will be considered. Chromosomes that are specified in `excludeChr` will not be included in the processed bin-level files. `excludeChr` argument is ignored if `useChrfile=TRUE`. Constructed bin-level files can be loaded into the R environment using the method `readBins`.

`constructBins` currently supports the following aligned read file formats for SET data (`PET = FALSE`): Eland result (`"eland_result"`), Eland extended (`"eland_extended"`), Eland export (`"eland_export"`), default Bowtie (`"bowtie"`), SAM (`"sam"`), `"bam"` (BAM), BED (`"bed"`), and CSEM (`"csem"`). For PET data (`PET = TRUE`), the following aligned read file formats are allowed: `"eland_result"` (Eland result), `"sam"` (SAM), and `"bam"` (BAM).

If input file format is neither BED nor CSEM BED, this method retains only reads mapping uniquely to the reference genome.

### Value

Processed bin-level files are exported to the directory specified in `outfileLoc`.

### Author(s)

Dongjun Chung, Pei Fen Kuan, Rene Welch, Sunduz Keles

### References

Kuan, PF, D Chung, JA Thomson, R Stewart, and S Keles (2011), "A Statistical Framework for the Analysis of ChIP-Seq Data", Journal of the American Statistical Association, Vol. 106, pp. 891-903.

Chung, D, Zhang Q, and Keles S (2014), "MOSAiCS-HMM: A model-based approach for detecting regions of histone modifications from ChIP-seq data", Datta S and Nettleton D (eds.), Statistical Analysis of Next Generation Sequencing Data, Springer.

### See Also

`readBins`, `BinData`.

### Examples

    ## Not run:
    library(mosaicsExample)

    constructBins( infile=system.file( file.path("extdata","wgEncodeBroadHistoneGm12878H3k4me3StdAlnRep1_chr22_sorted.bam"), package="mosaicsExample"),
        fileFormat="bam", outfileLoc="./",
        byChr=FALSE, useChrfile=FALSE, chrfile=NULL, excludeChr=NULL,
        PET=FALSE, fragLen=200, binSize=200, capping=0 )
    constructBins( infile=system.file( file.path("extdata","wgEncodeBroadHistoneGm12878ControlStdAlnRep1_chr22_sorted.bam"), package="mosaicsExample"),
        fileFormat="bam", outfileLoc="./",
        byChr=FALSE, useChrfile=FALSE, chrfile=NULL, excludeChr=NULL,
        PET=FALSE, fragLen=200, binSize=200, capping=0 )

    binHM <- readBins( type=c("chip","input"),
        fileName=c( "./wgEncodeBroadHistoneGm12878H3k4me3StdAlnRep1_chr22_sorted.bam_fragL200_bin200.txt",
        "./wgEncodeBroadHistoneGm12878ControlStdAlnRep1_chr22_sorted.bam_fragL200_bin200.txt" ) )
    binHM

    ## End(Not run)

[Package mosaics version 2.25.0 Index]