code correction

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 = "[email protected]", role = c("cre","aut")),
-          person("Walter Santana",  email = "[email protected]", role = c("aut")))
+          person("Aida Ghayour-Khiavi",  email = "[email protected]", role = c("aut")),
+          person("Matthew Dyer",  email = "[email protected]", role = c("aut")),
+          person("Walter Santana",  email = "[email protected]", role = c("aut")),
+          person("Touati Benoukraf",  email = "[email protected]", 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

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","//")  )