diff --git a/DESCRIPTION b/DESCRIPTION index 7ce5271..fac1f90 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,9 +1,12 @@ Package: forkedTF Type: Package Title: Creation of Forked-Position Weight Matrices, a graph model of multiple PWMs. -Version: 0.2.0 +Version: 1.2.0 Author: c(person("Roberto Tirado", email = "roberto@u.nus.edu", role = c("cre","aut")), - person("Walter Santana", email = "wsantana@lcg.unam.mx", role = c("aut"))) + person("Aida Ghayour-Khiavi", email = "aghayourkhia@mun.ca", role = c("aut")), + person("Matthew Dyer", email = "mjd443@mun.ca", role = c("aut")), + person("Walter Santana", email = "wsantana@lcg.unam.mx", role = c("aut")), + person("Touati Benoukraf", email = "tbenoukraf@mun.ca", role = c("aut"))) Depends: R (>= 3.6.0), methods Imports: graphics, grDevices, @@ -14,8 +17,7 @@ Imports: graphics, ggseqlogo (>= 0.1), cowplot (>= 1.0.0), grid (>= 3.6.1) -Description: More about what it does (maybe more than one line) - Use four spaces when indenting paragraphs within the Description. +Description: Current position weight matrices and sequence logos are not adequate to model transcription factor binding sites that are composed by a mixture of homodimer and heterodimer complexes. We introduce forkedTF, an R-library that combined functions to design Forked-Position Weight Matrices (FPWM) and Forked-Sequence Logos to better portray TF dimers. forkedTF uses and produces standard objects facilitating the exportation of FPWM to third-party software. License: GPL-3.0 Encoding: UTF-8 LazyData: true diff --git a/R/write.FPWM.R b/R/write.FPWM.R index 91aa327..f149c1b 100644 --- a/R/write.FPWM.R +++ b/R/write.FPWM.R @@ -48,7 +48,7 @@ write.FPWM <- function( FPWM = NULL, transfac_vector <- c( transfac_vector, paste0("parentLogo : ",FPWM@xid) ) transfac_vector <- c( transfac_vector, paste0("leafLogos : ", paste(unlist(FPWM@id),collapse=",")) ) transfac_vector <- c( transfac_vector, paste0("overlappingScore : ", paste(unlist(FPWM@score),collapse=",") ) ) - transfac_vector <- c( transfac_vector, paste0("numberOfBasePairs : ", paste(unlist(FPWM@nSites),collapse=",") ) ) + transfac_vector <- c( transfac_vector, paste0("numberOfMotifs : ", paste(unlist(FPWM@nSites),collapse=",") ) ) transfac_vector <- c( transfac_vector, paste0("numberOfOverlappingPeaks : ", paste(unlist(FPWM@nPeaks),collapse=",") ) ) transfac_vector <- c( transfac_vector, paste0("forkPosition : ",FPWM@forkPosition) ) transfac_vector <- c( transfac_vector, "XX", paste("P0","A","C","G","T",sep="\t") ) @@ -95,7 +95,7 @@ write.FPWM <- function( FPWM = NULL, } transfac_vector <- c( transfac_vector, c("XX","CC program: forkedTF") ) - transfac_vector <- c( transfac_vector, paste0("CC numberOfBasePairs: ",FPWM@nSites[ix]) ) + transfac_vector <- c( transfac_vector, paste0("CC numberOfMotifs: ",FPWM@nSites[ix]) ) transfac_vector <- c( transfac_vector, paste0("CC numberOfOverlappingPeaks: ",FPWM@nPeaks[ix]) ) transfac_vector <- c( transfac_vector, matrix_format ) transfac_vector <- c( transfac_vector, c("XX","//") )