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. |
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. |
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. |
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. |
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. |
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 |