LoadMotifLibrary: Load position weight matrices.

In chandlerzuo/atSNP: Affinity test for identifying regulatory SNPs

Description

Load the file for position weight matrices for motifs.

Usage

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 [e-mail], Chandler Zuo [e-mail]

Examples

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)

chandlerzuo/atSNP documentation built on Oct. 31, 2020, 4:33 a.m.