processBismarkAln {methylKit} | R Documentation

## Get methylation percentage from sorted Bismark alignments

### Description

The function calls methylation percentage per base from sorted Bismark SAM or BAM files and reads methylation information as methylKit objects. Bismark is a popular aligner for high-throughput bisulfite sequencing experiments and it outputs its results in SAM format by default, and can be converted to BAM. Bismark SAM/BAM format contains aligner specific tags which are absolutely necessary for methylation percentage calling using `processBismarkAln`. SAM/BAM files from other aligners will not work with this function.

### Usage

    processBismarkAln(
      location,
      sample.id,
      assembly,
      save.folder = NULL,
      save.context = c("CpG"),
      read.context = "CpG",
      nolap = FALSE,
      mincov = 10,
      minqual = 20,
      phred64 = FALSE,
      treatment = NULL,
      save.db = FALSE,
      verbose = 1
    )

    ## S4 method for signature 'character,character,character'
    processBismarkAln(
      location,
      sample.id,
      assembly,
      save.folder = NULL,
      save.context = c("CpG"),
      read.context = "CpG",
      nolap = FALSE,
      mincov = 10,
      minqual = 20,
      phred64 = FALSE,
      treatment = NULL,
      save.db = FALSE,
      verbose = 1
    )

    ## S4 method for signature 'list,list,character'
    processBismarkAln(
      location,
      sample.id,
      assembly,
      save.folder = NULL,
      save.context = c("CpG"),
      read.context = "CpG",
      nolap = FALSE,
      mincov = 10,
      minqual = 20,
      phred64 = FALSE,
      treatment = NULL,
      save.db = FALSE,
      verbose = 1
    )

### Arguments

`location` | location of sam or bam file(s). If multiple files are given this argument must be a list.
`sample.id` | the id(s) of samples in the same order as file. If multiple sam files are given this arugment must be a list.
`assembly` | string that determines the genome assembly. Ex: mm9,hg18 etc. This is just a string for book keeping. It can be any string. Although, when using multiple files from the same assembly, this string should be consistent in each object.
`save.folder` | The folder which will be used to save methylation call files, if set to NULL no methylation call file will be saved as a text file. The files saved can be read into R in less time using `methRead` function in `methylKit`
`save.context` | A character vector consisting following strings: "CpG","CHG","CHH". The methylation percentages for these methylation contexts will be saved to save.folder
`read.context` | One of the 'CpG','CHG','CHH' or 'none' strings. Determines what type of methylation context will be read-in to the memory which can be immediately used for analysis. If given as 'none', processBismarkAln will not return any object, but if a save.folder argument given it will save the methylation percentage call files.
`nolap` | if set to TRUE and the SAM/BAM file has paired-end reads, the one read of the overlapping paired-end read pair will be ignored for methylation calling.
`mincov` | minimum read coverage to call a methylation status for a base.
`minqual` | minimum phred quality score to call a methylation status for a base.
`phred64` | logical (default: FALSE) you will not need to set this TRUE, Currently bismark gives only phred33 scale
`treatment` | treatment vector only to be used when location and sample.id parameters are `list`s and you are trying to read-in multiple samples that are related to eachother in down-stream analysis.
`save.db` | A Logical to decide whether the resulting object should be saved as flat file database or not ( default: FALSE). With the default value, a text file containing methylation values will be saved. If TRUE, database will either be saved to location `save.folder` or if this is NULL, to a new folder in the current working directory named after this scheme: "methylDB <Date> <3randomlettersornumbers>"
`verbose` | logical set verbosity of methCall (default: TRUE)

### Value

`methylRaw` or `methylRawList` object

### Note

SAM files should be sorted with samtools sort or unix sort. Other sorting methods can alter the order of fields(columns) in the SAM file and that will result in an error when using `processBismarkAln()`.

### Examples

    # reading one bismark file:
    my.file=system.file("extdata", "test.fastq_bismark.sorted.min.sam",
                                  package = "methylKit")
    obj=processBismarkAln(my.file,"test",assembly="hg18",save.folder=NULL,
                     save.context="CpG",read.context="CpG")

    # reading multiple files
    file.list2=list(system.file("extdata", "test.fastq_bismark.sorted.min.sam",
    package = "methylKit"),
                   system.file("extdata", "test.fastq_bismark.sorted.min.sam",
                   package = "methylKit"),
                  system.file("extdata", "test.fastq_bismark.sorted.min.sam",
                  package = "methylKit"),
                   system.file("extdata", "test.fastq_bismark.sorted.min.sam",
                    package = "methylKit"))

     objs=processBismarkAln(location=file.list2
                 ,sample.id=list("test1","test2","ctrl1","ctrl1"),assembly="hg18",
                 save.folder=NULL,save.context=NULL,read.context="CpG",
                 nolap=FALSE,mincov=10,minqual=20,phred64=FALSE,
                 treatment=c(1,1,0,0))

[Package methylKit version 1.20.0 Index]