#### follow renaming of union classes in S4Vectors

Herve Pages authored on 01/02/2017 13:23:02
Showing 1 changed files
 ... ... @@ -1,7 +1,7 @@ 1 1  \name{gsnap-methods} 2 2  \docType{methods} 3 3  \alias{gsnap-methods} 4 -\alias{gsnap,character,characterORNULL,GsnapParam-method} 4 +\alias{gsnap,character,character_OR_NULL,GsnapParam-method} 5 5  \alias{gsnap} 6 6   7 7  \title{Align a Set of Reads Using the GSNAP Aligner} ... ... @@ -15,7 +15,7 @@ 15 15  } 16 16   17 17  \usage{ 18 -\S4method{gsnap}{character,characterORNULL,GsnapParam}(input_a, input_b, params, 18 +\S4method{gsnap}{character,character_OR_NULL,GsnapParam}(input_a, input_b, params, 19 19  output = file.path(getwd(), 20 20  file_path_sans_ext(basename(input_a), 21 21  TRUE)),

#### couple doc fixes

Michael Lawrence authored on 11/04/2014 18:40:32
Showing 1 changed files
 ... ... @@ -17,7 +17,8 @@ 17 17  \usage{ 18 18  \S4method{gsnap}{character,characterORNULL,GsnapParam}(input_a, input_b, params, 19 19  output = file.path(getwd(), 20 - file_path_sans_ext(input_a, TRUE)), 20 + file_path_sans_ext(basename(input_a), 21 + TRUE)), 21 22  consolidate = TRUE, ...) 22 23  } 23 24 

Michael Lawrence authored on 10/04/2014 19:40:59
Showing 1 changed files
 ... ... @@ -16,7 +16,8 @@ 16 16   17 17  \usage{ 18 18  \S4method{gsnap}{character,characterORNULL,GsnapParam}(input_a, input_b, params, 19 - output = file_path_sans_ext(input_a, TRUE), 19 + output = file.path(getwd(), 20 + file_path_sans_ext(input_a, TRUE)), 20 21  consolidate = TRUE, ...) 21 22  } 22 23 

#### update docs for change to output path determination

Michael Lawrence authored on 14/01/2014 19:12:33
Showing 1 changed files
 ... ... @@ -32,8 +32,8 @@ 32 32  will be saved in \code{dirname(output)}. If \code{split_output} in 33 33  \code{params} is \code{TRUE}, \code{basename(output)} is used as the 34 34  common stem for the multiple output files. Otherwise, the results 35 - are saved to \code{output} with the \dQuote{bam} extension 36 - appended. 35 + are saved to a single SAM file, its path formed by adding the 36 + \dQuote{sam} extention to \code{output}. 37 37  } 38 38  \item{consolidate}{If GSNAP is run with multiple worker threads, each 39 39  thread will output its own set of files. If consolidate is set to

#### clarify output parameter in documentation

 ... ... @@ -26,9 +26,15 @@ 26 26  is the only FASTA file used as input.} 27 27  \item{input_b}{If provided, a path to the FASTA file containing the 28 28  second set of reads from paired-end sequencing data.} 29 - \item{params}{A \code{GsnapParam} object to configure the behavior of GSNAP.} 30 - \item{output}{The output directory for the GSNAP alignments. If not 31 - provided, the directory is the same directory that contains input_a.} 29 + \item{params}{A \code{GsnapParam} object to configure the behavior of 30 + GSNAP.} 31 + \item{output}{The output path for the GSNAP alignments. The results 32 + will be saved in \code{dirname(output)}. If \code{split_output} in 33 + \code{params} is \code{TRUE}, \code{basename(output)} is used as the 34 + common stem for the multiple output files. Otherwise, the results 35 + are saved to \code{output} with the \dQuote{bam} extension 36 + appended. 37 + } 32 38  \item{consolidate}{If GSNAP is run with multiple worker threads, each 33 39  thread will output its own set of files. If consolidate is set to 34 40  TRUE, these files will be merged. The default is TRUE.}
 1 1 new file mode 100644 ... ... @@ -0,0 +1,43 @@ 1 +\name{gsnap-methods} 2 +\docType{methods} 3 +\alias{gsnap-methods} 4 +\alias{gsnap,character,characterORNULL,GsnapParam-method} 5 +\alias{gsnap} 6 + 7 +\title{Align a Set of Reads Using the GSNAP Aligner} 8 + 9 +\description{ 10 + Given a set of alignments, align them to a genome using the GSNAP 11 + algorithm. The GSNAP algorithm contains a number of features making it 12 + a very high quality algorithm for dealing with short reads and those 13 + from RNA-seq data in particular. Via the \code{GsnapParam} class 14 + and the \code{gsnap} function, R users are given complete control over GSNAP. 15 +} 16 + 17 +\usage{ 18 +\S4method{gsnap}{character,characterORNULL,GsnapParam}(input_a, input_b, params, 19 + output = file_path_sans_ext(input_a, TRUE), 20 + consolidate = TRUE, ...) 21 +} 22 + 23 +\arguments{ 24 + \item{input_a}{A path to the FASTA file containing reads to align against a 25 + \code{GmapGenome} object. If the sequencing data is single-end, this 26 + is the only FASTA file used as input.} 27 + \item{input_b}{If provided, a path to the FASTA file containing the 28 + second set of reads from paired-end sequencing data.} 29 + \item{params}{A \code{GsnapParam} object to configure the behavior of GSNAP.} 30 + \item{output}{The output directory for the GSNAP alignments. If not 31 + provided, the directory is the same directory that contains input_a.} 32 + \item{consolidate}{If GSNAP is run with multiple worker threads, each 33 + thread will output its own set of files. If consolidate is set to 34 + TRUE, these files will be merged. The default is TRUE.} 35 + \item{...}{Additional arguments to pass to GSNAP not specifically 36 + supported by the \code{gmapR} package.} 37 +} 38 + 39 +\value{ 40 + A \code{GsnapOutput} class. 41 +} 42 + 43 +\author{Michael Lawrence}