version 0.3.1

rtfbsdb/DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rtfbsdb
-Version: 0.3.0
-Date: 2015-12-02
+Version: 0.3.1
+Date: 2016-01-26
 Title: An Integrated Framework for Transcription Factor Binding Site Analysis
 Author: Charles G. Danko <[email protected]>, Zhong Wang<[email protected]>, Andre L. Martins<[email protected]>
 Maintainer: Zhong Wang<[email protected]>

rtfbsdb/R/create_tfbs.R

@@ -104,6 +104,7 @@ tfbs.dirs <- function(..., species="Homo_sapiens", args.read.motif = NULL, patte
 #' @return: NULL or tfbs object;
 
 tfbs_createFromCisBP <- function ( cisbp.db, 
+					motif_id    = NULL, 
 					tf_name     = NULL, 
 					tf_status   = NULL,
 					family_name = NULL, 
@@ -119,6 +120,7 @@ tfbs_createFromCisBP <- function ( cisbp.db,
 
 	tbm_f <- c();
 
+	if(!is.null(motif_id))   tbm_f <- c( tbm_f, paste( "tbm$Motif_ID=='", motif_id, "'", sep="") );
 	if(!is.null(tf_name))    tbm_f <- c( tbm_f, paste( "tbm$TF_Name=='", tf_name, "'", sep="") );
 	if(!is.null(tf_status))  tbm_f <- c( tbm_f, paste( "tbm$TF_Status=='", tf_status, "'", sep="") );
 	if(!is.null(family_name))tbm_f <- c( tbm_f, paste( "tbm$Family_Name=='", family_name, "'", sep="") );

rtfbsdb/R/scan_sites.R

@@ -19,6 +19,7 @@ extend.bed <- function( bed, len, file.twoBit )
 	chr_info <- get_chromosome_size( file.twoBit );
 	chr_max  <- chr_info[ match(chr, chr_info[,1]), 2 ];
 	ends[ ends >  chr_max ] <- chr_max[ ends >  chr_max ];
+	starts[ starts <=1 ] <- 1;
 
 	N = NCOL(bed);
 	if (N == 3) {

rtfbsdb/R/z_CisBP.R

@@ -380,7 +380,7 @@ setMethod("CisBP.getTFinformation", signature(cisbp.db="CisBP.db"),
 #' @return: tfbs object
 
 setGeneric("tfbs.createFromCisBP", 
-		def=function(cisbp.db, tf_name = NULL, tf_status = NULL, family_name = NULL, 
+		def=function(cisbp.db, motif_id = NULL, tf_name = NULL, tf_status = NULL, family_name = NULL, 
 					motif_type = NULL, msource_id =NULL, tf.information.type = 1){
 			stopifnot(class(cisbp.db) == "CisBP.db")
 			standardGeneric("tfbs.createFromCisBP")

rtfbsdb/man/tfbs.createFromCisBP.Rd

@@ -8,6 +8,7 @@ Build a tfbs object by querying the meta file of CisBP dataset and subsetting th
 }
 \usage{
 tfbs.createFromCisBP(cisbp.db, 
+      motif_id = NULL, 
       tf_name = NULL, 
       tf_status = NULL, 
       family_name = NULL, 
@@ -17,6 +18,7 @@ tfbs.createFromCisBP(cisbp.db,
 }
 \arguments{
   \item{cisbp.db}{A CisBP object(\code{"\linkS4class{CisBP.db}"}), including the file of TF_Information.txt.}
+  \item{motif_id}{String, indicating the Motif_ID field will be used to select motifs.}
   \item{tf_name}{String, indicating the TF_name field will be used to select motifs.}
   \item{tf_status}{String, indicating the TF_Status field will be used to select motifs. }
   \item{family_name}{String, indicating the Family_Name field will be used to select motifs. }

rtfbsdb/man/tfbs.scanTFsite.Rd

@@ -11,7 +11,7 @@ does not provided genome data such as hg19.2bit, mm10.2bit.
 tfbs.scanTFsite(tfbs, 
       file.twoBit, 
       gen.bed, 
-      return.type=c("matches", "posteriors", "maxposterior", "writedb"), 
+      return.type=c("matches", "maxscore", "posteriors", "maxposterior", "writedb"), 
       file.prefix=NA, 
       usemotifs = NA,
       ncores = 1, 
@@ -43,7 +43,7 @@ tfbs.scanTFsite(tfbs,
 \itemize{
 \item{matches:}{ returns all matching TF sites for all motifs.}
 \item{writedb:}{ writes a bed file with matches sites. Assumes that sort-bed and starch tools are availiable in $PATH}
-\item{maxscore:}{ returns the max score(poserior difference between motif model and background) in each bed-formatted loci.}
+\item{maxscore:}{ returns the max score(posterior difference between motif model and background) in each bed-formatted loci.}
 \item{posteriors:}{ returns the posteriors at each position in bed-formatted loci.}
 \item{maxposterior:}{ returns the max(posterior) in each bed-formatted loci.}
 }