ballgown-package |
The ballgown package for analysis of transcript assemblies |
annotate_assembly |
match assembled transcripts to annotated transcripts |
Ballgown |
Ballgown |
ballgown |
constructor function for ballgown objects |
ballgown-class |
Ballgown |
ballgown-constructor |
constructor function for ballgown objects |
ballgownp |
The ballgown package for analysis of transcript assemblies |
ballgownrsem |
load RSEM data into a ballgown object |
bg |
Toy ballgown object |
checkAssembledTx |
plot annotated and assembled transcripts together |
clusterTranscripts |
group a gene's assembled transcripts into clusters |
collapseTranscripts |
cluster a gene's transcripts and calculate cluster-level expression |
contains |
determine if one set of GRanges fully contains any of another set of GRanges |
dirs |
extract paths to tablemaker output |
dirs-method |
extract paths to tablemaker output |
eexpr |
extract exon-level expression measurements from ballgown objects |
eexpr-method |
extract exon-level expression measurements from ballgown objects |
expr |
extract expression components from ballgown objects |
expr-method |
extract expression components from ballgown objects |
expr<- |
Replacement method for expr slot in ballgown objects |
expr<--method |
Replacement method for expr slot in ballgown objects |
exprfilter |
subset ballgown objects using an expression filter |
geneIDs |
get gene IDs from a ballgown object |
geneIDs-method |
get gene IDs from a ballgown object |
geneNames |
get gene names from a ballgown object |
geneNames-method |
get gene names from a ballgown object |
getAttributeField |
extract a specific field of the "attributes" column of a data frame created from a GTF/GFF file |
getGenes |
label assembled transcripts with gene names |
gexpr |
extract gene-level expression measurements from ballgown objects |
gexpr-method |
extract gene-level expression measurements from ballgown objects |
gffRead |
read in GTF/GFF file as a data frame |
gffReadGR |
read in gtf file as GRanges object |
iexpr |
extract transcript-level expression measurements from ballgown objects |
iexpr-method |
extract transcript-level expression measurements from ballgown objects |
indexes |
extract the indexes from ballgown objects |
indexes-method |
extract the indexes from ballgown objects |
indexes<- |
Replace method for indexes slot in ballgown objects |
indexes<--method |
Replace method for indexes slot in ballgown objects |
last |
get the last element |
mergedDate |
extract package version & creation date from ballgown object |
mergedDate-method |
extract package version & creation date from ballgown object |
pctOverlap |
calculate percent overlap between two GRanges objects |
pData |
extract phenotype data from a ballgown object |
pData-method |
extract phenotype data from a ballgown object |
pData<- |
Replacement method for pData slot in ballgown objects |
pData<--method |
Replacement method for pData slot in ballgown objects |
plotLatentTranscripts |
cluster assembled transcripts and plot the results |
plotMeans |
visualize transcript abundance by group |
plotTranscripts |
visualize structure of assembled transcripts |
sampleNames |
get names of samples in a ballgown objects |
sampleNames-method |
get names of samples in a ballgown objects |
seqnames |
get sequence (chromosome) names from ballgown object |
seqnames-method |
get sequence (chromosome) names from ballgown object |
stattest |
statistical tests for differential expression in ballgown |
structure |
extract structure components from ballgown objects |
structure-method |
extract structure components from ballgown objects |
subset |
subset ballgown objects to specific samples or genomic locations |
subset-method |
subset ballgown objects to specific samples or genomic locations |
texpr |
extract transcript-level expression measurements from ballgown objects |
texpr-method |
extract transcript-level expression measurements from ballgown objects |
tGene |
Connect a transcript to its gene |
transcriptIDs |
get numeric transcript IDs from a ballgown object |
transcriptIDs-method |
get numeric transcript IDs from a ballgown object |
transcriptNames |
get transcript names from a ballgown object |
transcriptNames-method |
get transcript names from a ballgown object |
writeFiles |
write files to disk from ballgown object |