getRepeatTable {IntEREst} | R Documentation

## Get table of regions with repetetive DNA sequences

### Description

This function returns a data.frame that includes regions with repetetive DNA sequences. These sequences can bias the mapping of the reads to the genome excluding them will remove the bias.

### Usage

    getRepeatTable( dbUser="genome",
    	dbHost="genome-mysql.cse.ucsc.edu",	ucscGenome="hg19",
    	ucscTable="rmsk", minLength=0, repFamilyFil="Alu",
    	repFamilyCol="repFamily", repChrCol="genoName",
    	repBegCol="genoStart", repEndCol="genoEnd",
    	repStrandCol="strand", repNameCol="repName",
    	repClassCol="repClass")

### Arguments

`dbUser` | Database user name; set as "genome" by default.
`dbHost` | Database host address; set as "genome-mysql.cse.ucsc.edu" by default.
`ucscGenome` | The UCSC genome.
`ucscTable` | The UCSC table name. The table with repetetive sequences by default it is set as `"rmsk"`.
`minLength` | the minimum length criteria to consider the repetetive sequences. the default setting is `0`.
`repFamilyFil` | A vector including the repeats family to consider. By default the `"Alu"` elements are considered.
`repFamilyCol` | The name of the column of the input table (`ucscTable`) that represents the repeats family.
`repChrCol` | The column (either name or the number of the column) of the input table that represents the Chromosome names.
`repBegCol` | The column of the table that represents the start coordinates.
`repEndCol` | The column of the table that represents the end coordinates.
`repStrandCol` | The column of the table that represents the strand.
`repNameCol` | The column of the table representing the repeats' names.
`repClassCol` | The column of the table representing the repeats' classes.

### Value

Data frame with columns representing coordinates and annotations of repetitive DNA elements.

### Author(s)

Ali Oghabian

### Examples

    ## Not run:
    # Download table for Alu elemnts in the human genome
    suppressWarnings(repTable<- getRepeatTable(repFamilyFil="Alu",
    	ucscGenome="hg19"))

    ## End(Not run)

[Package IntEREst version 1.4.1 Index]