LoadMotifLibrary: Load position weight matrices.
In atSNP: Affinity test for identifying regulatory SNPs

Description Usage Arguments Details Value Author(s) Examples

Load the file for position weight matrices for motifs.

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LoadMotifLibrary(filename = NULL, urlname = NULL, tag = "MOTIF",
  transpose = FALSE, field = 2, sep = c("\t", " "), skipcols = 0,
  skiprows = 2, pseudocount = 0)

`filename`	a MEME format file name.
`urlname`	URL containing a MEME format file.
`tag`	A string that marks the description line of the position weight matrix.
`transpose`	If TRUE (default), then the position weight matrix should have 4 columns. Otherwise, it should have 4 rows.
`field`	The index of the field in the description line, seperated by space, that indicates the motif name.
`sep`	A vector of chars for the string separators to parse each lines of the matrix. Default: c(" ", "\t").
`skipcols`	Number of columns to be skipped in the position weight matrix.
`skiprows`	Number of description lines before each position weight matrix.
`pseudocount`	An integer for the pseudocount added to each of the original matrices. Default: 0. Recommended to be 1 if the original matrices are position frequency matrices.

This function reads the formatted file containing motif information and convert them into a list of position weight matrices. The list of arguments should provide enough flexibility of importing a varying number of formats. Some examples are the following: For MEME format, the suggested arguments are: tag = 'Motif', skiprows = 2, skipcols = 0, transpose = FALSE, field = 2, sep = ' '; For motif files from JOHNSON lab (i.e. http://johnsonlab.ucsf.edu/mochi_files/JASPAR_motifs_H_sapiens.txt), the suggested arguments are: tag = '/NAME', skiprows = 1, skipcols = 0, transpose = FALSE, field = 2, sep = "\t"; For JASPAR pfm matrices (i.e. http://jaspar.genereg.net/download/CORE/JASPAR 2018_CORE_vertebrates_non-redundant_pfms_jaspar.txt), the suggested arguments are: tag = ">", skiprows = 1, skipcols = 0, transpose = TRUE, field = 1, sep = "\t"; For the TRANSFAC library provided by UCF bioinformatics groups (i.e. http://gibbs.biomed.ucf.edu/PreDREM/download/nonredundantmotif.transfac ), the suggested arguments are: tag = "DE", skiprows = 1, skipcols = 1, transpose = FALSE, field = 2, sep = "\t".

A list object of position weight matrices.

Sunyoung Shin sunyoung.shin@utdallas.edu, Chandler Zuo chandler.c.zuo@gmail.com

pwms <- LoadMotifLibrary(
urlname="http://pages.stat.wisc.edu/~keles/atSNP-Data/pfm_vertebrates.txt", 
tag = ">", transpose = FALSE, field = 1, sep = c("\t", " ", ">"), 
skipcols = 1, skiprows = 1, pseudocount = 1)