getRepeatTable: Get table of regions with repetetive DNA sequences

Description Usage Arguments Value Author(s) Examples

View source: R/getRepeatTable.R

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

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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

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

## End(Not run)

IntEREst documentation built on Nov. 8, 2020, 8:05 p.m.