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


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Documentation for package ‘spliceSites’ version 1.31.0

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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 '['.