git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@103653 bc3139a8-67e5-0310-9ffc-ced21a209358
hpages@fhcrc.org authored on 11/05/2015 22:13:05
| ... | ... |
@@ -16,8 +16,8 @@ data.frame2GRanges(df, keepColumns = FALSE, ignoreStrand = FALSE) |
| 16 | 16 |
\code{seqnames}, \code{start}, \code{end} and optionally a
|
| 17 | 17 |
\code{strand column}.}
|
| 18 | 18 |
\item{keepColumns}{In case \code{df} has additional columns, should
|
| 19 |
- these columns be stored as metadata for the return GRanges or should |
|
| 20 |
- they be discarded.} |
|
| 19 |
+ these columns be stored as metadata columns on the return GRanges |
|
| 20 |
+ or should they be discarded.} |
|
| 21 | 21 |
\item{ignoreStrand}{In case \code{df} has a \code{strand} column,
|
| 22 | 22 |
should this column be ignored.} |
| 23 | 23 |
} |
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@78143 bc3139a8-67e5-0310-9ffc-ced21a209358
khansen authored on 06/07/2013 21:26:40
| ... | ... |
@@ -26,7 +26,7 @@ data.frame2GRanges(df, keepColumns = FALSE, ignoreStrand = FALSE) |
| 26 | 26 |
\code{names} for the return object.
|
| 27 | 27 |
} |
| 28 | 28 |
\value{
|
| 29 |
- An object of class \code{"GRanges"}
|
|
| 29 |
+ An object of class \code{GRanges}
|
|
| 30 | 30 |
} |
| 31 | 31 |
\author{
|
| 32 | 32 |
Kasper Daniel Hansen \email{khansen@jhsph.edu}
|
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@67929 bc3139a8-67e5-0310-9ffc-ced21a209358
m.carlson authored on 20/07/2012 17:45:09
| 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,38 @@ |
| 1 |
+\name{data.frame2GRanges}
|
|
| 2 |
+\alias{data.frame2GRanges}
|
|
| 3 |
+\title{
|
|
| 4 |
+ Converts a data frame to a GRanges. |
|
| 5 |
+} |
|
| 6 |
+\description{
|
|
| 7 |
+ Converting a data.frame to a GRanges object. The data.frame needs |
|
| 8 |
+ columns like chr, start and end (strand is optional). Additional |
|
| 9 |
+ columns may be kept in the GRanges object. |
|
| 10 |
+} |
|
| 11 |
+\usage{
|
|
| 12 |
+data.frame2GRanges(df, keepColumns = FALSE, ignoreStrand = FALSE) |
|
| 13 |
+} |
|
| 14 |
+\arguments{
|
|
| 15 |
+ \item{df}{A \code{data.frame} with columns \code{chr} or
|
|
| 16 |
+ \code{seqnames}, \code{start}, \code{end} and optionally a
|
|
| 17 |
+ \code{strand column}.}
|
|
| 18 |
+ \item{keepColumns}{In case \code{df} has additional columns, should
|
|
| 19 |
+ these columns be stored as metadata for the return GRanges or should |
|
| 20 |
+ they be discarded.} |
|
| 21 |
+ \item{ignoreStrand}{In case \code{df} has a \code{strand} column,
|
|
| 22 |
+ should this column be ignored.} |
|
| 23 |
+} |
|
| 24 |
+\note{
|
|
| 25 |
+ In case \code{df} has \code{rownames}, they will be used as
|
|
| 26 |
+ \code{names} for the return object.
|
|
| 27 |
+} |
|
| 28 |
+\value{
|
|
| 29 |
+ An object of class \code{"GRanges"}
|
|
| 30 |
+} |
|
| 31 |
+\author{
|
|
| 32 |
+ Kasper Daniel Hansen \email{khansen@jhsph.edu}
|
|
| 33 |
+} |
|
| 34 |
+\examples{
|
|
| 35 |
+df <- data.frame(chr = "chr1", start = 1:3, end = 2:4, |
|
| 36 |
+ strand = c("+","-","+"))
|
|
| 37 |
+data.frame2GRanges(df, ignoreStrand = TRUE) |
|
| 38 |
+} |