getRepeatTable: Get table of regions with repetetive DNA sequences
In IntEREst: Intron-Exon Retention Estimator

Description Usage Arguments Value Author(s) Examples

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.

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")

`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.

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

Ali Oghabian

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

## End(Not run)