regionCounts {methylKit} | R Documentation

## Get regional counts for given GRanges or GRangesList object

### Description

Convert `methylRaw`, `methylRawDB`, `methylRawList`, `methylRawListDB`, `methylBase` or `methylBaseDB` object into regional counts for a given `GRanges` or `GRangesList` object.

### Usage

    regionCounts(object,regions,cov.bases=0,strand.aware=FALSE,chunk.size,save.db,...)

    ## S4 method for signature 'methylRaw,GRanges'
    regionCounts(
      object,
      regions,
      cov.bases = 0,
      strand.aware = FALSE,
      chunk.size = 1e+06,
      save.db = FALSE,
      ...
    )

    ## S4 method for signature 'methylBase,GRanges'
    regionCounts(
      object,
      regions,
      cov.bases = 0,
      strand.aware = FALSE,
      chunk.size = 1e+06,
      save.db = FALSE,
      ...
    )

    ## S4 method for signature 'methylRaw,GRangesList'
    regionCounts(
      object,
      regions,
      cov.bases = 0,
      strand.aware = FALSE,
      chunk.size = 1e+06,
      save.db = FALSE,
      ...
    )

    ## S4 method for signature 'methylBase,GRangesList'
    regionCounts(
      object,
      regions,
      cov.bases = 0,
      strand.aware = FALSE,
      chunk.size = 1e+06,
      save.db = FALSE,
      ...
    )

    ## S4 method for signature 'methylRawList,GRanges'
    regionCounts(
      object,
      regions,
      cov.bases = 0,
      strand.aware = FALSE,
      chunk.size = 1e+06,
      save.db = FALSE,
      ...
    )

    ## S4 method for signature 'methylRawList,GRangesList'
    regionCounts(
      object,
      regions,
      cov.bases = 0,
      strand.aware = FALSE,
      chunk.size = 1e+06,
      save.db = FALSE,
      ...
    )

    ## S4 method for signature 'methylRawDB,GRanges'
    regionCounts(
      object,
      regions,
      cov.bases = 0,
      strand.aware = FALSE,
      chunk.size = 1e+06,
      save.db = TRUE,
      ...
    )

    ## S4 method for signature 'methylRawDB,GRangesList'
    regionCounts(
      object,
      regions,
      cov.bases = 0,
      strand.aware = FALSE,
      chunk.size = 1e+06,
      save.db = TRUE,
      ...
    )

    ## S4 method for signature 'methylRawListDB,GRanges'
    regionCounts(
      object,
      regions,
      cov.bases = 0,
      strand.aware = FALSE,
      chunk.size = 1e+06,
      save.db = TRUE,
      ...
    )

    ## S4 method for signature 'methylRawListDB,GRangesList'
    regionCounts(
      object,
      regions,
      cov.bases = 0,
      strand.aware = FALSE,
      chunk.size = 1e+06,
      save.db = TRUE,
      ...
    )

    ## S4 method for signature 'methylBaseDB,GRanges'
    regionCounts(
      object,
      regions,
      cov.bases = 0,
      strand.aware = FALSE,
      chunk.size = 1e+06,
      save.db = TRUE,
      ...
    )

    ## S4 method for signature 'methylBaseDB,GRangesList'
    regionCounts(
      object,
      regions,
      cov.bases = 0,
      strand.aware = FALSE,
      chunk.size = 1e+06,
      save.db = TRUE,
      ...
    )

### Arguments

`object` | a `methylRaw`, `methylRawDB`, `methylRawList`, `methylRawListDB`, `methylBase` or `methylBaseDB` object NOTE: The given regions (Granges/GrangesList object) will be orderd based on chromosome and position before searching for overlaps, so the resulting methylKit object might have a different ording than expected. See details section for the reasoning of this choice and ways to still get custom ordering of regions.
`regions` | a GRanges or GRangesList object. Make sure that the GRanges objects are unique in chr,start,end and strand columns.You can make them unique by using unique() function.
`cov.bases` | number minimum bases covered per region (Default:0). Only regions with base coverage above this threshold are returned.
`strand.aware` | if set to TRUE only CpGs that match the strand of the region will be summarized. (default:FALSE)
`chunk.size` | Number of rows to be taken as a chunk for processing the `methylDB` 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 “_regions” to current filename if database already exists or generate new file with filename “sampleID_regions” or “methylBase_filtered” dependent on input object `dbdir` The directory where flat file database(s) should be stored, defaults to getwd(), working directory for newly stored databases and to same 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

a new methylRaw,methylBase or methylRawList object. If `strand.aware` is set to FALSE (default). Even though the resulting object will have the strand information of `regions` it will still contain methylation information from both strands.

### Details

The given regions (Granges/GrangesList object) will be orderd based on chromosome and position before searching for overlaps, so the resulting methylKit object might have a different ording than expected. We are doing this is to ensure that resulting output is consistent for in-memory and database based objects, as database based objects always have to be sorted to enable tabix indexing and providing fast random access.

If you to still want get a custom ordering of the output regions you can access the single regions in any object providing your indices to the `select` or `extract` functions.

The parameter `chunk.size` is only used when working with `methylRawDB`, `methylBaseDB` 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`, `methylBaseDB` or `methylRawListDB`, while being per default FALSE for `methylRaw`, `methylBase` or `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 want to change the value of this parameter.

### Examples

    data(methylKit)

    # get the windows of interest as a GRanges object, this can be any set
    # of genomic locations
    library(GenomicRanges)
    my.win=GRanges(seqnames="chr21",
    ranges=IRanges(start=seq(from=9764513,by=10000,length.out=20),width=5000) )

    # getting counts per region
    regional.methylRaw=regionCounts(object=methylRawList.obj, regions=my.win,
    cov.bases=0,strand.aware=FALSE)

[Package methylKit version 1.16.1 Index]