make_template {JASPAR} | R Documentation |
Make a template that feeds into JASPAR databases
make_template(x, PARAM = NA, TAG = NA, sep = "\t", outFpre = NULL)
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 |
NA
A string of the template, and save it in output format of ‘.template’ and ‘.matrix’ if ‘outFpre’ specified.
Xiaobei Zhao
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))