Browse code

Added the seqbias package to the repository.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@52013 bc3139a8-67e5-0310-9ffc-ced21a209358

Chao-Jen Wong authored on 22/01/2011 00:26:36
Showing 1 changed files
1 1
new file mode 100644
... ...
@@ -0,0 +1,37 @@
1
+\name{seqbias.load}
2
+\alias{seqbias.load}
3
+\title{Loading seqbias models}
4
+\description{
5
+Loads a seqbias model from a file written with 'seqbias.save'.
6
+}
7
+\usage{seqbias.load(ref_fn, model_fn)}
8
+\arguments{
9
+    \item{ref_fn}{filename of a reference sequence against which the reads are
10
+    aligned in FASTA format.}
11
+    \item{model_fn}{filename of a saved seqbias model}
12
+}
13
+\details{
14
+    A large seqbias model can take some time (several minutes) to fit. It is
15
+    often preferable to do this just once. This function load the model from a
16
+    file in YAML format, having been written with 'seqbias.save'.
17
+}
18
+\value{A seqbias class.}
19
+\author{
20
+    Daniel Jones
21
+    \email{dcjones@cs.washington.edu}}
22
+\seealso{
23
+    \code{\link{seqbias.save}}
24
+}
25
+\examples{
26
+  reads_fn <- system.file( "extra/example.bam", package = "seqbias" )
27
+  ref_fn <- system.file( "extra/example.fa", package = "seqbias" )
28
+
29
+  sb <- seqbias.fit( ref_fn, reads_fn )
30
+
31
+  seqbias.save( sb, "my_seqbias_model.yml" )
32
+
33
+  # load sometime later
34
+  sb <- seqbias.load( ref_fn, "my_seqbias_model.yml" )
35
+}
36
+
37
+