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fixed doc issues

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1 parent bbfe398 commit f8ef833b270198594bc515e354d36210b9fe0bc6 @vsbuffalo committed Mar 19, 2012
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@@ -0,0 +1,5 @@
+\.git.*
+\.DS_Store
+\.RData
+\.Rbuildignore
+\.Rhistory
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@@ -1,5 +1,5 @@
Package: qrqc
-Version: 1.9.4
+Version: 1.9.5
Date: 2012-02-20
Title: Quick Read Quality Control
Author: Vince Buffalo
@@ -13,5 +13,5 @@ Description: Quickly scans reads and gathers statistics on base and quality
optional HTML quality report. S4 SequenceSummary objects allow specific tests
and functionality to be written around the data collected.
License: GPL (>=2)
-URL: http://bioinformatics.ucdavis.edu
+URL: http://github.com/vsbuffalo/qrqc
biocViews: Sequencing, QualityControl, DataImport, Preprocessing, Visualization, HighThroughputSequencing
View
@@ -6,7 +6,7 @@ setClass("SequenceSummary",
filename='character',
base.freqs='data.frame',
seq.lengths='integer',
- hash='integer',
+ hash='numeric',
hash.prop='numeric',
kmer='data.frame',
k='integer',
View
@@ -80,8 +80,12 @@ function(filename, type=c("fastq", "fasta"), max.length=1000, quality=c("sanger"
# hashed
obj@kmer <- local({
tmp <- unlist(out$kmer)
+ if (!is.finite(tmp))
+ warning(paste("Some k-mer counts are infinite, meaning there was",
+ "occurence of a k-mer over the maximum double size."))
kmer <- do.call(rbind, strsplit(names(tmp), '-'))
- data.frame(kmer=kmer[, 1], position=as.integer(kmer[, 2]), count=tmp, row.names=NULL)
+ data.frame(kmer=kmer[, 1], position=as.integer(kmer[, 2]),
+ count=as.numeric(tmp), row.names=NULL)
})
obj@hash.prop <- hash.prop
obj@k <- as.integer(k)
View
@@ -19,7 +19,7 @@
}
\arguments{
- \item{x}{an S4 object that inherits from \code{SequenceSummary} from
+ \item{x}{an S4 object that inherits from \code{\link[=SequenceSummary-class]{SequenceSummary}} from
\code{readSeqFile}.}
\item{geom}{Either "line", "bar", or "dodge" indicating
the geom to use when plotting the bases. "line" will plot base
@@ -76,7 +76,7 @@
geom_hline(yintercept=0.25, color="purple")
}
-\seealso{getBase,getBaseProp}
+\seealso{\code{\link{getBase}}, \code{\link{getBaseProp}}}
\keyword{methods}
\keyword{graphics}
View
@@ -8,7 +8,7 @@
\description{
\code{calcKL} takes in an object that inherits from
- \code{SequenceSummary} that has a kmers slot, and returns the terms of
+ \code{\link[=SequenceSummary-class]{SequenceSummary}} that has a kmers slot, and returns the terms of
the K-L divergence sum (which correspond to items in the sample space,
in this case, k-mers).
@@ -53,5 +53,6 @@
p + scale_y_continuous("K-L divergence")
}
+\seealso{\code{\link{kmerKLPlot}}, \code{\link{getKmer}}}
\keyword{methods}
\keyword{graphics}
View
@@ -50,7 +50,8 @@
gcPlot(s.trimmed.fastq) + geom_hline(yintercept=0.5, color="purple")
}
-\seealso{getBase,getBaseProp}
+\seealso{\code{\link{getBase}}, \code{\link{getBaseProp}}}
+
\keyword{methods}
\keyword{graphics}
View
@@ -3,8 +3,9 @@
\title{Use Line Segments and Points to Plot Quality Statistics by Position in the Read}
\description{
\code{geom_qlinerange} uses multiple line segments and points to plot
- quality ranges. By default the 10\% and 90\% range in plotted in grey, the quartile
- range in orange, and the mean as a point in blue.
+ quality ranges. By default the 10\% and 90\% range in plotted in grey,
+ the quartile range in orange, and the mean as a point in blue. It is
+ used in \code{\link{qualPlot}}.
}
\usage{
@@ -31,6 +32,6 @@ geom_qlinerange(extreme.color="grey", quartile.color="orange", mean.color="blue"
}
\author{Vince Buffalo <vsbuffalo@ucdavis.edu>}
-\seealso{getQual}
+\seealso{\code{\link{getQual}}, \code{\link{qualPlot}}}
\keyword{methods}
\keyword{graphics}
View
@@ -5,14 +5,14 @@
\alias{getBase,SequenceSummary-method}
\title{Get a Data Frame of Base Frequency Data from a \code{SequenceSummary} Object}
\description{
- An object that inherits from class \code{SequenceSummary} contains
- base frequency data by position gathered by \code{readSeqFile}. \code{getBase}
+ An object that inherits from class \code{\link[=SequenceSummary-class]{SequenceSummary}} contains
+ base frequency data by position gathered by \code{\link{readSeqFile}}. \code{\link{getBase}}
is an accessor function that reshapes the base frequency data by position
into a data frame.
This accessor function is useful if you want to map variables to
custom \code{ggplot2} aesthetics. Base proportions can be accessed
- with \code{getBaseProp}.
+ with \code{\link{getBaseProp}}.
}
@@ -57,6 +57,6 @@
}
-\seealso{getGC,getSeqlen,getBaseProp,getQual,getMCQual,basePlot}
+\seealso{\code{\link{getGC}}, \code{\link{getSeqlen}}, \code{\link{getBaseProp}}, \code{\link{getQual}}, \code{\link{getMCQual}}, \code{\link{basePlot}}}
\keyword{methods}
\keyword{accessor}
@@ -56,6 +56,7 @@
color=base)) + facet_grid(. ~ base) + scale_color_dna()
}
-\seealso{getGC,getSeqlen,getBase,getQual,getMCQual,basePlot}
+\seealso{\code{\link{getGC}}, \code{\link{getSeqlen}}, \code{\link{getBase}}, \code{\link{getQual}}, \code{\link{getMCQual}}, \code{\link{basePlot}}}
+
\keyword{methods}
\keyword{accessor}
View
@@ -5,15 +5,16 @@
\alias{getGC,SequenceSummary-method}
\title{Get a Data Frame of GC Content from a \code{SequenceSummary} object}
\description{
- An object that inherits from class \code{SequenceSummary} contains
- base frequency data by position gathered by \code{readSeqFile}. \code{getGC}
+ An object that inherits from class \code{\link[=SequenceSummary-class]{SequenceSummary}} contains
+ base frequency data by position gathered by
+ \code{\link{readSeqFile}}. \code{\link{getGC}}
is an accessor function that reshapes the base frequency data into a
data frame and returns the GC content by position.
This accessor function is useful if you want to map variables to
custom \code{ggplot2} aesthetics. Frequencies or proportions of all
- bases (not just GC) can be accessed with \code{getBase} and
- \code{getBaseProp} respectively.
+ bases (not just GC) can be accessed with \code{\link{getBase}} and
+ \code{\link{getBaseProp}} respectively.
}
\usage{
@@ -55,7 +56,9 @@
high="blue") + scale_y_continuous("GC content")
p
}
+\seealso{\code{\link{getSeqlen}}, \code{\link{getBase}},
+ \code{\link{getBaseProp}}, \code{\link{getQual}},
+ \code{\link{getMCQual}}, \code{\link{getKmer}}, \code{\link{gcPlot}}}
-\seealso{getSeqlen,getBase,getBaseProp,getQual,getMCQual,cPlot}
\keyword{methods}
\keyword{accessor}
View
@@ -7,9 +7,9 @@
\title{Get a Data Frame of k-mer Frequency by Position from a \code{SequenceSummary} Object}
\description{
- An object that inherits from class \code{SequenceSummary} contains
- k-mer frequency data by position gathered by \code{readSeqFile} when
- \code{kmer=TRUE}. \code{getKmer} is an accessor function that is
+ An object that inherits from class \code{\link[=SequenceSummary-class]{SequenceSummary}} contains
+ k-mer frequency data by position gathered by \code{\link{readSeqFile}} when
+ \code{kmer=TRUE}. \code{\link{getKmer}} is an accessor function that is
useful for custom \code{ggplot2} aesthetics.
}
@@ -51,6 +51,9 @@ getKmer(x)
fill=kmer), stat="identity")
p
}
-\seealso{getGC,getSeqlen,getBase,getBaseProp,getMCQual,kmerKLPlot,kmerEntropyPlot}
+\seealso{\code{\link{getGC}}, \code{\link{getSeqlen}}, \code{\link{getBase}},
+ \code{\link{getBaseProp}}, \code{\link{getQual}},
+ \code{\link{getMCQual}}, \code{\link{kmerKLPlot}}, \code{\link{kmerEntropyPlot}}}
+
\keyword{methods}
\keyword{accessor}
View
@@ -5,10 +5,11 @@
\alias{getMCQual,FASTQSummary-method}
\title{Get a Data Frame of Simulated Qualitied from a \code{FASTQSummary} object}
\description{
- An object that inherits from class \code{FASTQSummary} contains
- base quality data by position gathered by \code{readSeqFile}. \code{getMCQual}
- generates simulated quality data for each base from this binned
- quality data that can be used for adding smoothed lines via lowess.
+ An object that inherits from class \code{\link[=FASTQSummary-class]{FASTQSummary}} contains
+ base quality data by position gathered by
+ \code{\link{readSeqFile}}. \code{\link{getMCQual}} generates simulated
+ quality data for each base from this binned quality data that can be
+ used for adding smoothed lines via lowess.
This accessor function is useful if you want to map variables to
custom \code{ggplot2} aesthetics.
@@ -53,8 +54,7 @@
ymax=upper), color="grey") + geom_smooth(aes(x=position, y=quality),
data=getMCQual(s.fastq), color="blue", se=FALSE)
}
-
-\seealso{getGC,getSeqlen,getBase,getBasePropgetQual,qualPlot}
+\seealso{\code{\link{getGC}}, \code{\link{getSeqlen}}, \code{\link{getBase}}, \code{\link{getBaseProp}}, \code{\link{getQual}}, \code{\link{qualPlot}}}
\keyword{methods}
\keyword{accessor}
View
@@ -8,9 +8,8 @@
object}
\description{
- An object of class \code{FASTQSummary} contains quality
- data (binned by \code{readSeqFile}). \code{getQual} is an accessor
- function that reshapes the data into a data frame.
+ An object of class \code{\link[=FASTQSummary-class]{FASTQSummary}} contains quality data (binned by \code{\link{readSeqFile}}). \code{\link{getQual}} is
+ an accessor function that reshapes the data into a data frame.
This accessor function is useful if you want to map variables to
custom \code{ggplot2} aesthetics.
@@ -65,6 +64,9 @@ getQual(x)
p <- p + scale_color_gradient("mean quality", low="red", high="green")
p + scale_y_continuous("quality")
}
-\seealso{getGC,getSeqlen,getBase,getBaseProp,getMCQual,qualPlot}
+\seealso{\code{\link{getGC}}, \code{\link{getSeqlen}},
+ \code{\link{getBase}}, \code{\link{getBaseProp}},
+ \code{\link{getMCQual}}, \code{\link{qualPlot}}}
+
\keyword{methods}
\keyword{accessor}
View
@@ -56,7 +56,9 @@
color="blue") + scale_y_continuous("quality/count") + theme_bw()
}
-\seealso{getGC,getBase,getBaseProp,getQual,getMCQual,seqlenPlot}
+\seealso{\code{\link{getGC}}, \code{\link{getBase}},
+ \code{\link{getBaseProp}}, \code{\link{getQual}},
+ \code{\link{getMCQual}}, \code{\link{seqlenPlot}}}
\keyword{methods}
\keyword{accessor}
View
@@ -59,5 +59,6 @@
contaminated"=s.fastq, "random"=s.random.fasta))
}
+\seealso{\code{\link{getKmer}}, \code{\link{calcKL}}, \code{\link{kmerKLPlot}}}
\keyword{methods}
\keyword{graphics}
View
@@ -7,7 +7,7 @@
\title{Plot K-L Divergence Components for a Subset of k-mers to Inspect for Contamination}
\description{
- \code{kmerKLPlot} calls \code{calcKL}, which calculates the
+ \code{kmerKLPlot} calls \code{\link{calcKL}}, which calculates the
Kullback-Leibler divergence between the k-mer distribution at each
position compared to the k-mer distribution across all
positions. \code{kmerKLPlot} then plots each k-mer's contribution to
@@ -89,6 +89,7 @@
suppressWarnings(kmerKLPlot(list("highly contaminated"=s.contam.fastq, "less
contaminated"=s.fastq, "random"=s.random.fasta)))
}
-
+\seealso{\code{\link{getKmer}}, \code{\link{calcKL}},
+ \code{\link{kmerEntropyPlot}}}
\keyword{methods}
\keyword{graphics}
View
@@ -4,7 +4,7 @@
\alias{makeReport-methods}
\title{Make an HTML report from a FASTASummary of FASTQSummary object}
\description{
- \code{makeReport} takes a \code{FASTQSummary} or \code{FASTASummary}
+ \code{makeReport} takes a \code{\link[=FASTQSummary-class]{FASTQSummary}} or \code{\link[=FASTASummary-class]{FASTASummary}}
object, creates an HTML report, and writes it to a file within a
directory. The directory naming is incremental so past reports will
not be overwritten.
View
@@ -49,5 +49,5 @@
plotBases(s.fastq, type="prop")
}
}
-\seealso{basePlot}
+\seealso{\code{\link{basePlot}}}
\keyword{graphics}
View
@@ -1,3 +1,4 @@
+
\name{plotGC-methods}
\docType{methods}
\alias{plotGC}
@@ -24,5 +25,5 @@
plotGC(s.fastq)
}
}
-\seealso{gcPlot}
+\seealso{\code{\link{gcPlot}}}
\keyword{graphics}
View
@@ -44,6 +44,6 @@
plotQuals(s.fastq)
}
}
-\seealso{qualPlot}
+\seealso{\code{\link{qualPlot}}}
\keyword{graphics}
\keyword{methods}
View
@@ -24,5 +24,5 @@
plotSeqLengths(s.fastq)
}
}
-\seealso{seqlenPlot}
+\seealso{\code{\link{seqlenPlot}}}
\keyword{graphics}
View
@@ -73,6 +73,6 @@
qualPlot(list("not trimmed"=s.fastq, "trimmed"=s.trimmed.fastq))
}
-\seealso{getQual}
+\seealso{\code{\link{getQual}}}
\keyword{methods}
\keyword{graphics}
View
@@ -86,20 +86,22 @@
\code{\link[=FASTASummary-class]{FASTASummary}} are the classes of the
objects returned by \code{readSeqFile}.
- \code{\link{plotBases}} is a function that plots the distribution of
+ \code{\link{basePlot}} is a function that plots the distribution of
bases over sequence length for a particular \code{FASTASummary} or
- \code{FASTQSummary} object. \code{\link{plotGC}} combines and plots
+ \code{FASTQSummary} object. \code{\link{gcPlot}} combines and plots
the GC proportion.
- \code{\link{plotQuals}} is a function that plots the distribution of
+ \code{\link{qualPlot}} is a function that plots the distribution of
qualities over sequence length for a particular \code{FASTASummary}
or \code{FASTQSummary} object.
- \code{\link{plotSeqLengths}} is a function that plots a histogram of
+ \code{\link{seqlenPlot}} is a function that plots a histogram of
sequence lengths for a particular \code{FASTASummary} or
\code{FASTQSummary} object.
+ \code{\link{kmerKLPlot}} is a function that plots K-L divergence
+ of k-mers to look for possible biase in reads.
}
View
@@ -20,5 +20,5 @@ scale_color_dna()
color=base)) + scale_color_dna()
}
-\seealso{scale_color_iupac,plotBase}
+\seealso{\code{\link{scale_color_iupac}}, \code{\link{basePlot}}}
\keyword{graphics}
View
@@ -20,5 +20,5 @@ scale_color_iupac()
color=base)) + scale_color_iupac()
}
-\seealso{scale_color_dna,plotBase}
+\seealso{\code{\link{scale_color_dna}}, \code{\link{basePlot}}}
\keyword{graphics}
@@ -46,7 +46,7 @@
seqlenPlot(list("not trimmed"=s.fastq, "trimmed"=s.trimmed.fastq))
}
-\seealso{getSeqlen}
+\seealso{\code{\link{getSeqlen}}}
\keyword{methods}
\keyword{graphics}
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