Fixed manual and more bugs

.Rbuildignore

@@ -1,2 +1,4 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^doc$
+^Meta$

.gitignore

@@ -3,3 +3,6 @@ data/tx_hg38.RData
 .Rproj.user
 *.RData
 *.Rproj
+inst/doc
+doc
+Meta

DESCRIPTION

@@ -25,7 +25,8 @@ Depends:
     R (>= 3.5.0)
 Suggests:
     knitr,
-    testthat
+    testthat,
+    rmarkdown
 License: GPL-3 | file LICENSE
 LazyData: false
 RoxygenNote: 6.1.1

R/helper.R

@@ -280,7 +280,7 @@ DownsampleTxLoc <- function(txLoc1, txLoc2, seed = NULL) {
     if (!is.null(seed)) set.seed(seed)
 
     # Subsample
-    loci <- mapply(
+    loci <- Map(
         function(loci1, loci2) loci1[sample.int(nrow(loci1), nrow(loci2)), ],
         GetLoci(txLoc1),
         GetLoci(txLoc2))
@@ -342,7 +342,7 @@ SubsampleTxLoc <- function(txLoc, fractions, seed = NULL) {
     if (!is.null(seed)) set.seed(seed)
 
     # Subsample
-    loci <- mapply(
+    loci <- Map(
         function(loci, frac) {
             idx <- sample.int(nrow(loci), round(frac * nrow(loci)))
             loci[idx, ]
@@ -437,7 +437,7 @@ GetRelDistNearest <- function(lst1, lst2) {
     stopifnot(identical(names(lst1), names(lst2)))
 
     # Calculate nearest distances from start
-    lst <- mapply(
+    lst <- Map(
         function(gr1, gr2) {
 
             # Collapse range of gr1 and gr2 to the start coordinate

R/methods.R

@@ -145,14 +145,16 @@ SmartMap.ToTx <- function(gr,
 #'
 #' @param gr A \code{GRanges} object; specifies the list of of genomic features
 #' to be mapped.
-#' @param id A character string; specifies a name for loci from \code{gr}; if
-#' \code{NULL} then \code{id = ""}; default is \code{NULL}.
-#' @param refGenome A character string; specifies a specific reference genome
-#' assembly version based on which the matching transcriptome is loaded;
+#' @param id A \code{character} string; specifies a name for loci from 
+#' \code{gr}; if \code{NULL} then \code{id = ""}; default is \code{NULL}.
+#' @param refGenome A \code{character} string; specifies a specific reference 
+#' genome assembly version based on which the matching transcriptome is loaded;
 #' default is \code{"hg38"}.
-#' @param ignore.strand A logical scalar; if \code{TRUE} strand information is
-#' ignored when mapping genome coordinates to transcript coordinates; default
-#' is \code{FALSE}.
+#' @param ignore.strand A \code{logical} scalar; if \code{TRUE} strand 
+#' information is ignored when mapping genome coordinates to transcript 
+#' coordinates; default is \code{FALSE}.
+#' @param showPb A \code{logical} scalar; if \code{TRUE} show a progress bar; 
+#' default is \code{TRUE}.
 #'
 #' @return A \code{txLoc} object. See 'Details'.
 #'
@@ -172,7 +174,8 @@ SmartMap.ToTx <- function(gr,
 SmartMap <- function(gr,
                      id = NULL,
                      refGenome = "hg38",
-                     ignore.strand = FALSE) {
+                     ignore.strand = FALSE,
+                     showPb = TRUE) {
 
     # Sanity check
     CheckClass(gr, "GRanges")
@@ -203,7 +206,7 @@ SmartMap <- function(gr,
     loci <- SmartMap.ToTx(
         gr, txBySec, seqBySec, geneXID,
         ignore.strand = ignore.strand,
-        showPb = TRUE)
+        showPb = showPb)
 
     # Return `txLoc` object
     new("txLoc",
@@ -254,17 +257,17 @@ SmartMap <- function(gr,
 #' null sites using this approach.
 #'
 #' @param txLoc A \code{txLoc} object.
-#' @param id A character string; identifier for null sites; if \code{NULL} then
-#' \code{id = "null"}; default is \code{NULL}.
-#' @param method A character string; specifies the method used to the generate
-#' null distribution; if \code{method == "ntAbund"} the position of all
-#' nucleotides specified by \code{nt} will be used as null sites; if
+#' @param id A \code{character} string; identifier for null sites; if 
+#' \code{NULL} then \code{id = "null"}; default is \code{NULL}.
+#' @param method A \code{character} string; specifies the method used to the 
+#' generate null distribution; if \code{method == "ntAbund"} the position of 
+#' all nucleotides specified by \code{nt} will be used as null sites; if
 #' \code{method == "perm"} (DEPRECATED, see 'Details') then null sites will be
 #' generated by uniform-randomly shuffling candidatepositions from \code{locus}
 #' within the corresponding transcript region; default is \code{"ntAbund"}.
-#' @param nt A single character; if \code{method == "ntAbund"}, use \code{nt}
-#' to derive distribution of null sites.
-#' @param showPb A logical scalar; if \code{TRUE} show a progress
+#' @param nt A single \code{character}; if \code{method == "ntAbund"}, use 
+#' \code{nt} to derive distribution of null sites.
+#' @param showPb A \code{logical} scalar; if \code{TRUE} show a progress
 #' bar; default is \code{TRUE}.
 #'
 #' @return A \code{txLoc} object. See 'Details'.
@@ -337,7 +340,7 @@ GenerateNull <- function(txLoc,
         pb <- txtProgressBar(
             max = length(GetRegions(txLoc)), style = 3, width = 60)
 
-    loci <- mapply(
+    loci <- Map(
         function(i, region) {
 
           # Update progress bar
@@ -470,7 +473,7 @@ GetGC <- function(txLoc, flank = 10) {
 
         # Extract subsequences
         # We use `subseq` instead of `substr` as it is more performant
-        seqWindow <- as(mapply(
+        seqWindow <- as(Map(
             function(seq, x) subseq(seq, start = x[1], end = x[2]),
             seqRegion, windows), "DNAStringSet")
 
@@ -643,7 +646,7 @@ GetSplicingSites <- function(refGenome = "hg38", filter = c("CDS", "5'UTR")) {
       # corresponding to splicing donor and acceptor sites
       # Add score and id metadata columns to make sure that we are
       # consistent with the BED6 format
-      junct <- unlist(as(mapply(
+      junct <- unlist(as(Map(
         function(fix, type) {
           eej <- resize(
             junct, width = 1, fix = fix, ignore.strand = F, use.names = T)
@@ -895,7 +898,9 @@ GetDistanceStartStop <- function(txLoc, refGenome = "hg38") {
 #' that are allowed during the motif matching; default is 0.
 #' @param showPb A logical scalar; if \code{TRUE} show a progress bar; default
 #' is \code{TRUE}.
-
+#' 
+#' @return A \code{txLoc} object.
+#' 
 #' @author Maurits Evers, \email{maurits.evers@@anu.edu.au}
 #'
 #' @import GenomicRanges IRanges

R/plot.R

@@ -517,7 +517,7 @@ PlotSpatialEnrichment <- function(txLoc.pos,
     breaks <- seq(0, posMax, by = binWidth)
 
     # Plot
-    invisible(mapply(
+    invisible(Map(
         function(loci.pos, loci.neg, region) {
 
             # Store site positions
@@ -546,7 +546,7 @@ PlotSpatialEnrichment <- function(txLoc.pos,
                 ctsMat <- as.matrix(rbind(ctsPos, ctsNeg))
                 rownames(ctsMat) <- c(GetId(txLoc.pos), GetId(txLoc.neg))
                 title <- sprintf(
-                    "%s\nN(%s) = %i, N(%s) = %i, bw = %i nt, window = %i nt",
+                    "%s\nN(%s) = %i, N(%s) = %i\nbw = %i nt, window = %i nt",
                     region,
                     GetId(txLoc.pos),
                     sum(ctsPos),
@@ -1147,7 +1147,7 @@ PlotSeqLogo <- function(txLoc, flank = 5, ylim = c(0, 2)) {
         par(mfrow = c(ceiling(length(GetRegions(txLoc)) / 2), 2))
     }
 
-    mapply(
+    invisible(Map(
         function(locus, region) {
 
             # Define window coordinates
@@ -1202,6 +1202,6 @@ PlotSeqLogo <- function(txLoc, flank = 5, ylim = c(0, 2)) {
                    bty = "n")
 
         },
-        GetLoci(txLoc), GetRegions(txLoc))
+        GetLoci(txLoc), GetRegions(txLoc)))
 
 }