Manages align gap positions from RNA-seq data

Documentation for package ‘spliceSites’ version 1.2.0

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

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

-- A --

aaGapSites-class	Class '"aaGapSites"'
addGeneAlignPart	Reads a bamRange object for a given 'bamReader', 'refGenome' and gene name.
addGeneAlignPart-method	Reads a bamRange object for a given 'bamReader', 'refGenome' and gene name.
addHbond	Class '"hbond"'
addHbond-method	Class '"hbond"'
addHbond-methods	Class '"hbond"'
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_X_ranks functions
alt_left_ranks-method	alt_X_ranks functions
alt_left_ranks-methods	alt_X_ranks functions
alt_ranks	alt_X_ranks functions
alt_ranks-method	alt_X_ranks functions
alt_ranks-methods	alt_X_ranks functions
alt_right_ranks	alt_X_ranks functions
alt_right_ranks-method	alt_X_ranks functions
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"'

-- 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"'
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"'
dim-methods	'dim': Return dimensions of contained data.frame.
dnaGapSites	Creating 'gapSites' and 'dnaGapSites' objects.
dnaGapSites-class	Class '"dnaGapSites"'
dnaGapSites-method	Creating 'gapSites' and 'dnaGapSites' objects.
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"'

-- 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"'
getAnnStrand	Class '"gapSites"'
getAnnStrand-method	Class '"gapSites"'
getAnnStrand-methods	Class '"gapSites"'
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"'
getProfile-method	Class '"gapSites"'
getProfile-methods	Class '"gapSites"'
getSequence	Class '"cdRanges"'
getSequence-method	Class '"caRanges"'
getSequence-method	Class '"cdRanges"'
getSequence-methods	Class '"cdRanges"'
gptm	Class '"gapSites"'
gptm-method	Class '"gapSites"'
gptm-methods	Class '"gapSites"'

-- 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"'
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"'
lend-method	Class '"gapSites"'
lend-methods	Class '"gapSites"'
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"'
lstart-method	Class '"gapSites"'
lstart-methods	Class '"gapSites"'

-- M --

maxEnt-class	Class '"maxEnt"'
merge-methods	'merge' Merging two objects into one.
merge.gapSites	Class '"gapSites"'

-- N --

nAlignGaps	Class '"gapSites"'
nAlignGaps-method	Class '"gapSites"'
nAlignGaps-methods	Class '"gapSites"'
nAligns	Class '"gapSites"'
nAligns-method	Class '"gapSites"'
nAligns-methods	Class '"gapSites"'

-- O --

overlap_genome

Class '"gapSites"'

-- P --

plot_diff	Class '"annGapSites"'
plot_diff-method	Class '"annGapSites"'
plot_diff-methods	Class '"annGapSites"'
plot_diff_ranks	alt_X_ranks functions
plot_diff_ranks-method	alt_X_ranks functions
plot_diff_ranks-methods	alt_X_ranks functions

-- 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 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"'
rend-method	Class '"gapSites"'
rend-methods	Class '"gapSites"'
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"'
rpmg-method	Class '"gapSites"'
rpmg-methods	Class '"gapSites"'
rstart	Class '"gapSites"'
rstart-method	Class '"gapSites"'
rstart-methods	Class '"gapSites"'

-- 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"'
seqid-method	Class '"cRanges"': Centered ranges.
seqid-method	Class '"gapSites"'
seqid-methods	Class '"gapSites"'
seqlogo	Class '"cdRanges"'
seqlogo-method	Class '"cdRanges"'
seqlogo-method	Class '"dnaGapSites"'
seqlogo-methods	Class '"cdRanges"'
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"'
silic_tryp	silic_tryp function
sortTable	Class '"cRanges"': Centered ranges.
sortTable-method	Class '"cRanges"': Centered ranges.
sortTable-method	Class '"gapSites"'
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"'
strand-methods	Class '"cRanges"': Centered ranges.
strand<--method	Class '"gapSites"'

-- 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"'
write.annDNA.tables-method	Class '"gapSites"'
write.annDNA.tables-methods	Class '"gapSites"'
write.files	write.files
write.files-method	Class '"aaGapSites"'
write.files-method	Class '"caRanges"'
write.files-methods	write.files

-- misc --

[-methods

Methods for Function '['.