| 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 |