make_template: Make a template that feeds into JASPAR databases

In JASPAR: R modules for JASPAR databases: a collection of transcription factor DNA-binding preferences, modeled as matrices.

Description

Make a template that feeds into JASPAR databases

Usage

  make_template(x, PARAM = NA, TAG = NA, sep = "\t",
    outFpre = NULL)

Arguments

x	matrix, the pfm
PARAM	a list, the PARAM(s)
TAG	a list, the TAG(s)
sep	a string, the delimiter
outFpre	a string, a file path to save

Details

NA

Value

A string of the template, and save it in output format of ‘.template’ and ‘.matrix’ if ‘outFpre’ specified.

Author(s)

Xiaobei Zhao

Examples

x <-
  rbind(
        c(3, 0, 0, 0, 0, 0),
        c(8, 0, 23, 0, 0, 0),
        c(2, 23, 0, 23, 0, 24),
        c(11, 1, 1, 1, 24, 0)
        )

PARAM <-
  list(
       INT_ID=NULL,
       BASE_ID="MA0006",
       COLLECTION="CORE",
       VERSION=1,
       NAME="Arnt-Ahr",
       SPECIES="10090")
TAG <-
  list(
       class="bHLH",
       medline="7592839",
       tax_group="vertebrate",
       sysgroup="vertebrate",
       acc="P30561",
       acc="P53762",
       comment="dimer",
       type="SELEX",
       newest=1
       )
cat(make_template(x=x,PARAM=PARAM,TAG=TAG))

JASPAR documentation built on May 2, 2019, 6:24 a.m.