getRepeatTable {IntEREst} | R Documentation |
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 |
minLength |
the minimum length criteria to consider the repetetive sequences. the default
setting is |
repFamilyFil |
A vector including the repeats family to consider. By default the |
repFamilyCol |
The name of the column of the input table ( |
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)