updatePFAM:
Process raw UCSC PFAM table
Description
Truncates and maps the contents of the raw hg19 UCSC PFAM table
Usage
updatePFAM(raw.file = "ucscGenePfam.txt", search.dir = getwd(),
file.name = "", ID2DE = FALSE)
Arguments
raw.file
Filename of raw PFAM table
search.dir
Directory in which the raw.file should be located
file.name
Filename of the processed table
ID2DE
Controls mapping from PFAM identification for Accession number to its definition
Value
Produces a truncated tab-delimited text file named file.name in search.dir.Returns the processed file name if a file was created, FALSE otherwise.
Details
The protein domain table can be obtained by downloading from the hg19 annotation database of UCSC (see default raw.file), or extracting data using the UCSC Table Browser Tool.
References
Karolchik D, et al. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 2004;32:D493-D496.