Last data update: 2014.03.03
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SMO (statistical methods ontology)
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A class for representing reads from next-generation sequencing experiments that have been aligned to genomic intervals.
● Data Source:
BioConductor
● Keywords: classes
● Alias: AlignedGenomeIntervals, AlignedGenomeIntervals-class, [,AlignedGenomeIntervals,ANY,ANY-method, c,AlignedGenomeIntervals-method, c.AlignedGenomeIntervals, chrlengths, chrlengths,AlignedGenomeIntervals-method, chrlengths<-, chrlengths<-,AlignedGenomeIntervals,numeric-method, chromosome,AlignedGenomeIntervals-method, chromosome,Genome_intervals-method, clusters,AlignedGenomeIntervals-method, clusters,Genome_intervals-method, coerce,AlignedGenomeIntervals,RangedData-method, coerce,AlignedRead,AlignedGenomeIntervals-method, coverage,AlignedGenomeIntervals-method, detail,AlignedGenomeIntervals-method, export, export,AlignedGenomeIntervals,character,character-method, export,Genome_intervals,character,ANY-method, extend, extend,AlignedGenomeIntervals-method, extend,Genome_intervals-method, extend,Genome_intervals_stranded-method, hist,AlignedGenomeIntervals-method, id,AlignedGenomeIntervals-method, id<-, id<-,AlignedGenomeIntervals,character-method, interval_included,AlignedGenomeIntervals,AlignedGenomeIntervals-method, interval_included,AlignedGenomeIntervals,Genome_intervals_stranded-method, interval_included,Genome_intervals_stranded,AlignedGenomeIntervals-method, interval_overlap,AlignedGenomeIntervals,AlignedGenomeIntervals-method, interval_overlap,AlignedGenomeIntervals,Genome_intervals-method, interval_overlap,AlignedGenomeIntervals,Genome_intervals_stranded-method, interval_overlap,Genome_intervals,AlignedGenomeIntervals-method, interval_overlap,Genome_intervals_stranded,AlignedGenomeIntervals-method, matches, matches,AlignedGenomeIntervals-method, matches<-, matches<-,AlignedGenomeIntervals,integer-method, nchar,AlignedGenomeIntervals-method, organism, organism,AlignedGenomeIntervals-method, organism<-, organism<-,AlignedGenomeIntervals,character-method, organism<-,AlignedGenomeIntervals-method, plot,AlignedGenomeIntervals,ANY-method, plot,AlignedGenomeIntervals,Genome_intervals_stranded-method, plot,AlignedGenomeIntervals,missing-method, plot,AlignedGenomeIntervals-method, reads, reads,AlignedGenomeIntervals-method, reads<-, reads<-,AlignedGenomeIntervals,character-method, reduce,AlignedGenomeIntervals-method, reduce,Genome_intervals-method, sample,AlignedGenomeIntervals-method, score,AlignedGenomeIntervals-method, score<-, score<-,AlignedGenomeIntervals,numeric-method, score<-,AlignedGenomeIntervals-method, seqnames, seqnames,AlignedGenomeIntervals-method, show,AlignedGenomeIntervals-method, sort,AlignedGenomeIntervals-method, strand,AlignedGenomeIntervals-method, strand<-,AlignedGenomeIntervals,factor-method, strand<-,AlignedGenomeIntervals,vector-method, subset, subset,AlignedGenomeIntervals-method, summary, summary,AlignedGenomeIntervals-method, width,AlignedGenomeIntervals-method
●
2 images
Function to create AlignedGenomeIntervals objects from BAM (binary alignment map format) files. Uses functions from package Rsamtools to parse BAM files.
● Data Source:
BioConductor
countReadsAnnotated
(Package: girafe ) :
Sum up aligned reads per category of genome feature
● Data Source:
BioConductor
● Keywords: manip
● Alias: countReadsAnnotated
●
1 images
fracOverlap
(Package: girafe ) :
Retrieve intervals overlapping by fraction of width
● Data Source:
BioConductor
getFeatureCounts
(Package: girafe ) :
get the read counts for a supplied set of genomic features
● Data Source:
BioConductor
Called internally by other girafe functions. Normally need not be called by the user.
● Data Source:
BioConductor
intPhred
(Package: girafe ) :
Extract integer Phred score values from FastQ data
● Data Source:
BioConductor
● Keywords: manip
● Alias: intPhred
●
1 images
medianByPosition
(Package: girafe ) :
Compute median quality for each nucleotide position
● Data Source:
BioConductor
addNBSignificance
(Package: girafe ) :
assess significance of sliding-window read counts
p -value to each window based on the number of aligned reads in the window. The p -values can be corrected for multiple testing using any of the correction methods implemented for p.adjust.
● Data Source:
BioConductor
perWindow
(Package: girafe ) :
Investigate aligned reads in genome intervals with sliding
● Data Source:
BioConductor
providing 
.