# A bioconductor package for exploration of alignment gap positions from RNA-seq data

## Documentation for package ‘spliceSites’ version 1.26.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E G H I K L M N O P R S T U W misc

spliceSites-package | Calculate information on splice-sites from gapped alignments in RNA-seq data.

## -- A --

aaGapSites-class | Class '"aaGapSites"'
addGeneAligns | Reads a bamRange object for a given 'bamReader', 'refGenome' and gene name.
addGeneAligns-method | Reads a bamRange object for a given 'bamReader', 'refGenome' and gene name.
addGenomeData | Add MaxEnt-scores, Exon-Intron junction sequences score to Feature Data in 'ExpressionSet' object.
addGenomeData-method | Add MaxEnt-scores, Exon-Intron junction sequences score to Feature Data in 'ExpressionSet' object.
addGenomeData-method | Add MaxEnt-scores, Exon-Intron junction sequences score to Feature Data in 'gapSites' object.
addHbond | Class '"hbond"': Provides data and functions for calculation of HBond scores for 5' splice-sites.
addHbond-method | Class '"hbond"': Provides data and functions for calculation of HBond scores for 5' splice-sites.
addHbond-methods | Class '"hbond"': Provides data and functions for calculation of HBond scores for 5' splice-sites.
addKeyTable | Class '"keyProfiler"'
addKeyTable-method | Class '"keyProfiler"'
addKeyTable-methods | Class '"keyProfiler"'
addMaxEnt | addMaxEnt: Extract subset of data contained in given range given object.
addMaxEnt-method | addMaxEnt: Extract subset of data contained in given range given object.
addMaxEnt-methods | addMaxEnt: Extract subset of data contained in given range given object.
alignGapList | Read 'gapSites'
alt_left_ranks | alt_left_ranks and alt_right_ranks functions: Identification of alternative splicing events from gapped alignments.
alt_left_ranks-method | alt_left_ranks and alt_right_ranks functions: Identification of alternative splicing events from gapped alignments.
alt_left_ranks-methods | alt_left_ranks and alt_right_ranks functions: Identification of alternative splicing events from gapped alignments.
alt_ranks | alt_left_ranks and alt_right_ranks functions: Identification of alternative splicing events from gapped alignments.
alt_ranks-method | alt_left_ranks and alt_right_ranks functions: Identification of alternative splicing events from gapped alignments.
alt_ranks-methods | alt_left_ranks and alt_right_ranks functions: Identification of alternative splicing events from gapped alignments.
alt_right_ranks | alt_left_ranks and alt_right_ranks functions: Identification of alternative splicing events from gapped alignments.
alt_right_ranks-method | alt_left_ranks and alt_right_ranks functions: Identification of alternative splicing events from gapped alignments.
annGapSites-class | Class '"annGapSites"'
annotate | Annotation functions for 'gapSites' objects
annotate-method | Adds annotation data to existing ExpressionSet (created by 'readExpSet')
annotate-method | Annotation functions for 'gapSites' objects
annotate-methods | Annotation functions for 'gapSites' objects
annotation | Annotation functions for 'gapSites' objects
annotation-method | Annotation functions for 'gapSites' objects
annotation-methods | Annotation functions for 'gapSites' objects
annotation<- | Annotation functions for 'gapSites' objects
annotation<--method | Annotation functions for 'gapSites' objects
annotation<--methods | Annotation functions for 'gapSites' objects
appendKeyTable | Class '"keyProfiler"'
appendKeyTable-method | Class '"keyProfiler"'
appendKeyTable-methods | Class '"keyProfiler"'
as.data.frame-methods | 'as.data.frame' Returning content of data.frame.
as.data.frame.cRanges | Class '"cRanges"': Centered ranges.
as.data.frame.gapSites | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.

## -- B --

basedir-method | Class '"hbond"'
basedir-method | Class '"maxEnt"'
basedir<--method | Class '"hbond"'
basedir<--method | Class '"maxEnt"'

## -- C --

c-method | Class '"cRanges"': Centered ranges.
c-method | Class '"caRanges"'
c-method | Class '"cdRanges"'
c-method | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
c-methods | Coercing functions 'c'.
caRanges-class | Class '"caRanges"'
cdRanges-class | Class '"cdRanges"'
count | Class '"cRanges"': Centered ranges.
count-method | Class '"cRanges"': Centered ranges.
count-methods | Class '"cRanges"': Centered ranges.
countByGeneName | Reads align number for selected gene from multiple BAM-files.
cRanges-class | Class '"cRanges"': Centered ranges.

## -- D --

dim-method | Class '"cRanges"': Centered ranges.
dim-method | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
dim-methods | 'dim': Return dimensions of contained data.frame.
dnaGapSites | Creating 'gapSites' and 'dnaGapSites' objects.
dnaGapSites-class | Class '"dnaGapSites"'
dnaGapSites-method | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
dnaGapSites-methods | Creating 'gapSites' and 'dnaGapSites' objects.
dnaRanges | Reads a bamRange object for a given 'bamReader', 'refGenome' and gene name.
dnaRanges-method | Reads a bamRange object for a given 'bamReader', 'refGenome' and gene name.
dnaRanges-methods | Reads a bamRange object for a given 'bamReader', 'refGenome' and gene name.
do_group_align_data | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.

## -- E --

end-method | Class '"cRanges"': Centered ranges.
extractByGeneName | extractByGeneName: Extract subset for sites which lie in range(s) defined by given gene list.
extractByGeneName-method | extractByGeneName: Extract subset for sites which lie in range(s) defined by given gene list.
extractByGeneName-methods | extractByGeneName: Extract subset for sites which lie in range(s) defined by given gene list.
extractRange | extractRange: Extract subset from object where records lie in given range.
extractRange-method | extractRange: Extract subset from object where records lie in given range.
extractRange-methods | extractRange: Extract subset from object where records lie in given range.

## -- G --

gapSites | Creating 'gapSites' and 'dnaGapSites' objects.
gapSites-class | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
getAnnStrand | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
getAnnStrand-method | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
getAnnStrand-methods | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
getGapSites | Read 'gapSites'
getKeyTable | Class '"keyProfiler"'
getKeyTable-method | Class '"keyProfiler"'
getKeyTable-methods | Class '"keyProfiler"'
getMeStrand | addMaxEnt: Extract subset of data contained in given range given object.
getMeStrand-method | addMaxEnt: Extract subset of data contained in given range given object.
getMeStrand-methods | addMaxEnt: Extract subset of data contained in given range given object.
getProfile | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
getProfile-method | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
getProfile-methods | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
getSequence | Class '"cdRanges"'
getSequence-method | Class '"caRanges"'
getSequence-method | Class '"cdRanges"'
getSequence-methods | Class '"cdRanges"'
gptm | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
gptm-method | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
gptm-methods | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.

## -- H --

hbond | Class '"hbond"'
hbond-class | Class '"hbond"'
hbond-method | Class '"hbond"'
hbond-methods | Class '"hbond"'
head-method | Class '"aaGapSites"'
head-method | Class '"cRanges"': Centered ranges.
head-method | Class '"caRanges"'
head-method | Class '"cdRanges"'
head-method | Class '"dnaGapSites"'
head-method | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
head-methods | 'head' Return first lines of contained data.frame.

## -- I --

id | Class '"cRanges"': Centered ranges.
id-method | Class '"cRanges"': Centered ranges.
id-methods | Class '"cRanges"': Centered ranges.
initialize-method | Class '"SpliceCountSet"'
initialize-method | Class '"cRanges"': Centered ranges.
initialize-method | Class '"cdRanges"'
initialize-method | Class '"keyProfiler"'
initialize-methods | 'initialize' Initializing objects.

## -- K --

keyProfiler-class | Class '"keyProfiler"'

## -- L --

lCodons | xCodon methods
lCodons-method | xCodon methods
lCodons-methods | xCodon methods
lend | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
lend-method | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
lend-methods | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
lJunc | xJunc methods: lJunc, rJunc, lrJunc
lJunc-method | xJunc methods: lJunc, rJunc, lrJunc
lJunc-methods | xJunc methods: lJunc, rJunc, lrJunc
lJuncStrand | xJuncStrand methods: lJuncStrand, rJuncStrand, lrJuncStrand
lJuncStrand-method | xJuncStrand methods: lJuncStrand, rJuncStrand, lrJuncStrand
lJuncStrand-methods | xJuncStrand methods: lJuncStrand, rJuncStrand, lrJuncStrand
load.hbond | Class '"hbond"'
load.maxEnt | Class '"maxEnt"'
lrCodons | lrCodon methods
lrCodons-method | lrCodon methods
lrCodons-methods | lrCodon methods
lrJunc | xJunc methods: lJunc, rJunc, lrJunc
lrJunc-method | xJunc methods: lJunc, rJunc, lrJunc
lrJunc-methods | xJunc methods: lJunc, rJunc, lrJunc
lrJuncStrand | xJuncStrand methods: lJuncStrand, rJuncStrand, lrJuncStrand
lrJuncStrand-method | xJuncStrand methods: lJuncStrand, rJuncStrand, lrJuncStrand
lrJuncStrand-methods | xJuncStrand methods: lJuncStrand, rJuncStrand, lrJuncStrand
lstart | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
lstart-method | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
lstart-methods | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.

## -- M --

maxEnt-class | Class '"maxEnt"'
merge-methods | 'merge' Merging two objects into one.
merge.gapSites | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.

## -- N --

nAlignGaps | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
nAlignGaps-method | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
nAlignGaps-methods | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
nAligns | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
nAligns-method | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
nAligns-methods | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.

## -- O --

overlap_genome | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.

## -- P --

plotGeneAlignDepth | plotGeneAlignDepth: Plots of read alignment depth for genetic regions
plotGeneAlignDepth-method | plotGeneAlignDepth: Plots of read alignment depth for genetic regions
plotGeneAlignDepth-methods | plotGeneAlignDepth: Plots of read alignment depth for genetic regions
plot_diff | Class '"annGapSites"'
plot_diff-method | Class '"annGapSites"'
plot_diff-methods | Class '"annGapSites"'
plot_diff_ranks | alt_left_ranks and alt_right_ranks functions: Identification of alternative splicing events from gapped alignments.
plot_diff_ranks-method | alt_left_ranks and alt_right_ranks functions: Identification of alternative splicing events from gapped alignments.
plot_diff_ranks-methods | alt_left_ranks and alt_right_ranks functions: Identification of alternative splicing events from gapped alignments.

## -- R --

rangeByGeneName | Reads a bamRange object for a given 'bamReader', 'refGenome' and gene name.
rCodons | xCodon methods
rCodons-method | xCodon methods
rCodons-methods | xCodon methods
readCuffGeneFpkm | Reads FPKM values into ExpressionSet.
readExpSet | Reads align number or gptm or rpmg value from all given BAM-files and all identified align gaps into ExpressionSet.
readMergedBamGaps | Reads an object of type 'gapSites' using a vector of BAM file names.
readTabledBamGaps | readTabledBamGaps function
rend | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
rend-method | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
rend-methods | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
resize_left | trim and resize methods: trim_left, trim_right, resize_left, resize_right
resize_left-method | trim and resize methods: trim_left, trim_right, resize_left, resize_right
resize_left-methods | trim and resize methods: trim_left, trim_right, resize_left, resize_right
resize_right | trim and resize methods: trim_left, trim_right, resize_left, resize_right
resize_right-method | trim and resize methods: trim_left, trim_right, resize_left, resize_right
resize_right-methods | trim and resize methods: trim_left, trim_right, resize_left, resize_right
rJunc | xJunc methods: lJunc, rJunc, lrJunc
rJunc-method | xJunc methods: lJunc, rJunc, lrJunc
rJunc-methods | xJunc methods: lJunc, rJunc, lrJunc
rJuncStrand | xJuncStrand methods: lJuncStrand, rJuncStrand, lrJuncStrand
rJuncStrand-method | xJuncStrand methods: lJuncStrand, rJuncStrand, lrJuncStrand
rJuncStrand-methods | xJuncStrand methods: lJuncStrand, rJuncStrand, lrJuncStrand
rpmg | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
rpmg-method | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
rpmg-methods | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
rstart | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
rstart-method | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
rstart-methods | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.

## -- S --

saveMaxEnt | Class '"maxEnt"'
saveMaxEnt-method | Class '"maxEnt"'
saveMaxEnt-methods | Class '"maxEnt"'
score3 | Class '"maxEnt"'
score3-method | Class '"maxEnt"'
score3-methods | Class '"maxEnt"'
score5 | Class '"maxEnt"'
score5-method | Class '"maxEnt"'
score5-methods | Class '"maxEnt"'
scoreSeq3 | Class '"maxEnt"'
scoreSeq3-method | Class '"maxEnt"'
scoreSeq3-methods | Class '"maxEnt"'
scoreSeq5 | Class '"maxEnt"'
scoreSeq5-method | Class '"maxEnt"'
scoreSeq5-methods | Class '"maxEnt"'
seqid | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
seqid-method | Class '"cRanges"': Centered ranges.
seqid-method | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
seqid-methods | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
seqlogo | seqlogo: Plotting sequence logo for 'cdRanges' and 'dnaGapSites' objects.
seqlogo-method | Class '"dnaGapSites"'
seqlogo-method | seqlogo: Plotting sequence logo for 'cdRanges' and 'dnaGapSites' objects.
seqlogo-methods | seqlogo: Plotting sequence logo for 'cdRanges' and 'dnaGapSites' objects.
setMeStrand | addMaxEnt: Extract subset of data contained in given range given object.
setMeStrand-method | addMaxEnt: Extract subset of data contained in given range given object.
setMeStrand-methods | addMaxEnt: Extract subset of data contained in given range given object.
show-method | Class '"aaGapSites"'
show-method | Class '"cRanges"': Centered ranges.
show-method | Class '"dnaGapSites"'
show-method | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
silic_tryp | silic_tryp function
sortTable | Class '"cRanges"': Centered ranges.
sortTable-method | Class '"cRanges"': Centered ranges.
sortTable-method | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
sortTable-methods | Sorting contained data with 'sortTable'.
SpliceCountSet-class | Class '"SpliceCountSet"'
spliceSites | Calculate information on splice-sites from gapped alignments in RNA-seq data.
start-method | Class '"cRanges"': Centered ranges.
strand | Class '"cRanges"': Centered ranges.
strand-method | Class '"cRanges"': Centered ranges.
strand-method | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
strand-methods | Class '"cRanges"': Centered ranges.
strand<--method | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.

## -- T --

translate | Class '"cdRanges"'
translate-method | Class '"cdRanges"'
translate-method | Class '"dnaGapSites"'
translate-methods | Class '"cdRanges"'
trim_left | trim and resize methods: trim_left, trim_right, resize_left, resize_right
trim_left-method | trim and resize methods: trim_left, trim_right, resize_left, resize_right
trim_left-methods | trim and resize methods: trim_left, trim_right, resize_left, resize_right
trim_right | trim and resize methods: trim_left, trim_right, resize_left, resize_right
trim_right-method | trim and resize methods: trim_left, trim_right, resize_left, resize_right
trim_right-methods | trim and resize methods: trim_left, trim_right, resize_left, resize_right
truncateSeq | truncateSeq method
truncateSeq-method | truncateSeq method
truncateSeq-methods | truncateSeq method
truncate_seq | truncate_seq function
trypsinCleave | trypsinCleave method
trypsinCleave-method | trypsinCleave method
trypsinCleave-methods | trypsinCleave method

## -- U --

uniqueJuncAnn | uniqueJuncAnn method for ExpressionSet
uniqueJuncAnn-method | uniqueJuncAnn method for ExpressionSet
uniqueJuncAnn-methods | uniqueJuncAnn method for ExpressionSet

## -- W --

width-method | Class '"cRanges"': Centered ranges.
write.annDNA.tables | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
write.annDNA.tables-method | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
write.annDNA.tables-methods | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
write.files | write.files
write.files-method | Class '"aaGapSites"'
write.files-method | Class '"caRanges"'
write.files-methods | write.files

## -- misc --

[-method | Class '"gapSites"': Container for tabulated alignment gap positions on RNA-seq data.
[-methods | Methods for Function '['.