fixed row.names when subsetting the data.frame

From: Caleb Lareau <lareauc@Calebs-MacBook-Pro.local>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/diffloop@117023 bc3139a8-67e5-0310-9ffc-ced21a209358

Author: c.lareau

R/annotation.R

@@ -215,7 +215,7 @@ setMethod(f = "getHumanTSS", signature = c("character", "ANY"),
 
 #' Annotate loops as Enhancer-Promoter or CTCF-CTCF
 #'
-#' \code{annotateLoops} adds a column to the results slot of a loops
+#' \code{annotateLoops} adds a column to the rowData slot of a loops
 #' object categorizing loops as either e-p (enhancer-promoter), ctcf 
 #' (CTCF-CTCF) or none (no biological annotation). If both ctcf and e-p,
 #' then categorized as e-p. 
@@ -231,7 +231,7 @@ setMethod(f = "getHumanTSS", signature = c("character", "ANY"),
 #' @param enhancer GRanges object corresponding to locations of enhancer peaks
 #' @param promoter GRanges object corresponding to locations of promoter regions
 #'
-#' @return A loops object with an additional row 'loop.type' in the results slot
+#' @return A loops object with an additional row 'loop.type' in the rowData slot
 #'
 #' @examples
 #' rda<-paste(system.file('rda',package='diffloop'),'loops.small.rda',sep='/')

R/core.R

@@ -270,8 +270,8 @@ setMethod(f = "subsetRegion", signature = c("loops", "GRanges",
     intsdf <- as.data.frame(dlo@interactions)
 
     # Update interactions indices
-    lm <- mapping[match(intsdf$left, mapping$queryHits), 2, drop=F]
-    rm <- mapping[match(intsdf$right,mapping$queryHits), 2, drop=F]
+    lm <- mapping[match(intsdf$left, mapping$queryHits), 2, drop=FALSE]
+    rm <- mapping[match(intsdf$right,mapping$queryHits), 2, drop=FALSE]
 
     # Format new indices matrix
     totalupdate <- cbind(unlist(lm), unlist(rm))
@@ -282,15 +282,15 @@ setMethod(f = "subsetRegion", signature = c("loops", "GRanges",
     # Subset rowData
     newRowData <- as.data.frame(dlo@rowData[cc, ])
     colnames(newRowData) <- colnames(dlo@rowData)
+    row.names(newRowData) <- NULL
 
     # Grab counts indicies; removes lines that don't map to
     # anything via making them NAs and then removing them
     newcounts <- matrix(dlo@counts[cc], ncol = ncol(dlo@counts))
     colnames(newcounts) <- colnames(dlo@counts)
 
     # Update values
-    slot(dlo, "anchors", check = TRUE) <- dlo@anchors[keepTheseAnchors, 
-        ]
+    slot(dlo, "anchors", check = TRUE) <- dlo@anchors[keepTheseAnchors, ]
     slot(dlo, "interactions", check = TRUE) <- newinteractions
     slot(dlo, "counts", check = TRUE) <- newcounts
     slot(dlo, "rowData", check = TRUE) <- newRowData
@@ -306,8 +306,8 @@ setMethod(f = "subsetRegion", signature = c("loops", "GRanges",
     intsdf <- as.data.frame(dlo@interactions)
 
     # Update interaction indicies
-    lm <- mapping[match(intsdf$left, mapping$queryHits), 2, drop=F]
-    rm <- mapping[match(intsdf$right,mapping$queryHits), 2, drop=F]
+    lm <- mapping[match(intsdf$left, mapping$queryHits), 2, drop=FALSE]
+    rm <- mapping[match(intsdf$right,mapping$queryHits), 2, drop=FALSE]
 
     # Format new indices matrix
     totalupdate <- cbind(unlist(lm), unlist(rm))
@@ -323,6 +323,8 @@ setMethod(f = "subsetRegion", signature = c("loops", "GRanges",
     # Subset rowData
     newRowData <- as.data.frame(dlo@rowData[cc, ])
     colnames(newRowData) <- colnames(dlo@rowData)
+    row.names(newRowData) <- NULL
+
 
     # Update values
     slot(dlo, "anchors", check = TRUE) <- newAnchors