Genome Intervals and Read Alignments for Functional Exploration

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Documentation for package ‘girafe’ version 1.42.0

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addNBSignificance assess significance of sliding-window read counts
agiFromBam Create AlignedGenomeIntervals objects from BAM files.
AlignedGenomeIntervals Class 'AlignedGenomeIntervals'
AlignedGenomeIntervals-class Class 'AlignedGenomeIntervals'
c-method Class 'AlignedGenomeIntervals'
c.AlignedGenomeIntervals Class 'AlignedGenomeIntervals'
chrlengths Class 'AlignedGenomeIntervals'
chrlengths-method Class 'AlignedGenomeIntervals'
chrlengths<- Class 'AlignedGenomeIntervals'
chrlengths<--method Class 'AlignedGenomeIntervals'
chromosome-method Class 'AlignedGenomeIntervals'
clusters-method Class 'AlignedGenomeIntervals'
coerce-method Class 'AlignedGenomeIntervals'
countReadsAnnotated Sum up aligned reads per category of genome feature
coverage-method Class 'AlignedGenomeIntervals'
detail-method Class 'AlignedGenomeIntervals'
estimateNBParams assess significance of sliding-window read counts
export Class 'AlignedGenomeIntervals'
export-method Class 'AlignedGenomeIntervals'
extend Class 'AlignedGenomeIntervals'
extend-method Class 'AlignedGenomeIntervals'
fracOverlap Retrieve intervals overlapping by fraction of width
hist-method Class 'AlignedGenomeIntervals'
id-method Class 'AlignedGenomeIntervals'
id<- Class 'AlignedGenomeIntervals'
id<--method Class 'AlignedGenomeIntervals'
interval_included-method Class 'AlignedGenomeIntervals'
interval_overlap-method Class 'AlignedGenomeIntervals'
intPhred Extract integer Phred score values from FastQ data
matches Class 'AlignedGenomeIntervals'
matches-method Class 'AlignedGenomeIntervals'
matches<- Class 'AlignedGenomeIntervals'
matches<--method Class 'AlignedGenomeIntervals'
medianByPosition Compute median quality for each nucleotide position
nchar-method Class 'AlignedGenomeIntervals'
organism Class 'AlignedGenomeIntervals'
organism-method Class 'AlignedGenomeIntervals'
organism<- Class 'AlignedGenomeIntervals'
organism<--method Class 'AlignedGenomeIntervals'
perWindow Investigate aligned reads in genome intervals with sliding windows
plot-method Class 'AlignedGenomeIntervals'
reads Class 'AlignedGenomeIntervals'
reads-method Class 'AlignedGenomeIntervals'
reads<- Class 'AlignedGenomeIntervals'
reads<--method Class 'AlignedGenomeIntervals'
reduce-method Class 'AlignedGenomeIntervals'
sample-method Class 'AlignedGenomeIntervals'
score-method Class 'AlignedGenomeIntervals'
score<- Class 'AlignedGenomeIntervals'
score<--method Class 'AlignedGenomeIntervals'
seqnames Class 'AlignedGenomeIntervals'
seqnames-method Class 'AlignedGenomeIntervals'
show-method Class 'AlignedGenomeIntervals'
sort-method Class 'AlignedGenomeIntervals'
strand-method Class 'AlignedGenomeIntervals'
strand<--method Class 'AlignedGenomeIntervals'
subset Class 'AlignedGenomeIntervals'
subset-method Class 'AlignedGenomeIntervals'
summary Class 'AlignedGenomeIntervals'
summary-method Class 'AlignedGenomeIntervals'
trimAdapter Remove 3' adapter contamination
which_nearest Methods for function 'which_nearest' and genome intervals
which_nearest-method Methods for function 'which_nearest' and genome intervals
width-method Class 'AlignedGenomeIntervals'
[-method Class 'AlignedGenomeIntervals'