filterByCoverage {methylKit} | R Documentation

## Filter methylRaw, methylRawDB, methylRawList and methylRawListDB object based on read coverage

### Description

This function filters `methylRaw`, `methylRawDB`, `methylRawList` and `methylRawListDB` objects. You can filter based on lower read cutoff or high read cutoff. Higher read cutoff is usefull to eliminate PCR effects Lower read cutoff is usefull for doing better statistical tests.

### Usage

    filterByCoverage(methylObj, lo.count = NULL, lo.perc = NULL,
      hi.count = NULL, hi.perc = NULL, chunk.size = 1e+06, save.db = FALSE,
      ...)

    ## S4 method for signature 'methylRaw'
    filterByCoverage(methylObj, lo.count = NULL,
      lo.perc = NULL, hi.count = NULL, hi.perc = NULL, chunk.size = 1e+06,
      save.db = FALSE, ...)

    ## S4 method for signature 'methylRawList'
    filterByCoverage(methylObj, lo.count = NULL,
      lo.perc = NULL, hi.count = NULL, hi.perc = NULL, chunk.size = 1e+06,
      save.db = FALSE, ...)

    ## S4 method for signature 'methylRawDB'
    filterByCoverage(methylObj, lo.count = NULL,
      lo.perc = NULL, hi.count = NULL, hi.perc = NULL, chunk.size = 1e+06,
      save.db = TRUE, ...)

    ## S4 method for signature 'methylRawListDB'
    filterByCoverage(methylObj, lo.count = NULL,
      lo.perc = NULL, hi.count = NULL, hi.perc = NULL, chunk.size = 1e+06,
      save.db = TRUE, ...)

### Arguments

`methylObj` | a `methylRaw`, `methylRawDB`, `methylRawList` or `methylRawListDB` object
`lo.count` | An integer for read counts.Bases/regions having lower coverage than this count is discarded
`lo.perc` | A double [0-100] for percentile of read counts. Bases/regions having lower coverage than this percentile is discarded
`hi.count` | An integer for read counts. Bases/regions having higher coverage than this is count discarded
`hi.perc` | A double [0-100] for percentile of read counts. Bases/regions having higher coverage than this percentile is discarded
`chunk.size` | Number of rows to be taken as a chunk for processing the `methylRawDB` or `methylRawListDB` objects, default: 1e6
`save.db` | A Logical to decide whether the resulting object should be saved as flat file database or not, default: explained in Details sections
`...` | optional Arguments used when save.db is TRUE `suffix` A character string to append to the name of the output flat file database, only used if save.db is true, default actions: append “_filtered” to current filename if database already exists or generate new file with filename “sampleID_filtered” `dbdir` The directory where flat file database(s) should be stored, defaults to getwd(), working directory for newly stored databases and to original directory for already existing database `dbtype` The type of the flat file database, currently only option is "tabix" (only used for newly stored databases)

### Value

`methylRaw`, `methylRawDB`, `methylRawList` or `methylRawListDB` object depending on input object

### Details

The parameter `chunk.size` is only used when working with `methylRawDB` or `methylRawListDB` objects, as they are read in chunk by chunk to enable processing large-sized objects which are stored as flat file database. Per default the chunk.size is set to 1M rows, which should work for most systems. If you encounter memory problems or have a high amount of memory available feel free to adjust the `chunk.size`.

The parameter `save.db` is per default TRUE for methylDB objects as `methylRawDB` and `methylRawListDB`, while being per default FALSE for `methylRaw` and `methylRawList`. If you wish to save the result of an in-memory-calculation as flat file database or if the size of the database allows the calculation in-memory, then you might change the value of this parameter.

### Examples

    data(methylKit)

    # filter out bases with covereage above 500 reads
    filtered1=filterByCoverage(methylRawList.obj,lo.count=NULL,lo.perc=NULL,
    hi.count=500,hi.perc=NULL)

    # filter out bases with cread coverage above 99.9th percentile of coverage
    # distribution
    filtered2=filterByCoverage(methylRawList.obj,lo.count=NULL,lo.perc=NULL,
    hi.count=NULL,hi.perc=99.9)

    # filter out bases with covereage above 500 reads and save to database
    # "test1_max500.txt.bgz"
    # in directory "methylDB", filtered3 now becomes a \code{methylRawDB} object
    filtered3=filterByCoverage(methylRawList.obj[[1]], lo.count=NULL,lo.perc=NULL,
                               hi.count=500, hi.perc=NULL, save.db=TRUE,
                               suffix="max500", dbdir="methylDB")

    # tidy up
    rm(filtered3)
    unlink("methylDB",recursive=TRUE)

[Package methylKit version 1.6.3 Index]