LoadMotifLibrary: Load position weight matrices.

Description Usage Arguments Details Value Author(s) Examples

View source: R/motif_analysis.R

Description

Load the file for position weight matrices for motifs.

Usage

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

Arguments

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.

Details

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".

Value

A list object of position weight matrices.

Author(s)

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

Examples

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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)

atSNP documentation built on April 28, 2020, 6:50 p.m.