| 26c90635 |
import(methods)
importMethodsFrom(Biostrings, reverseComplement, matchPattern,
DNAString)
|
| 87fafb1a |
importMethodsFrom(Seqinfo, seqlengths, "seqlengths<-",
|
| 26c90635 |
"seqlevels<-")
importFrom(RColorBrewer, brewer.pal)
importFrom(Rsamtools, scanBamFlag)
importMethodsFrom(Rsamtools, scanBam, ScanBamParam)
importFrom(VGAM, vsmooth.spline, zeta)
importFrom(data.table, data.table, setkey, setnames)
importFrom(qvalue, qvalue)
importFrom(sqldf, sqldf)
importFrom(stats, lm, pchisq, pnorm, smooth.spline)
importFrom(utils, write.table)
import(IRanges, GenomicRanges, rtracklayer)
|
| 92a6ade7 |
exportClasses(
|
| d059853f |
"r3Cseq","r3CseqInBatch"
|
| 92a6ade7 |
)
|
| 26c90635 |
|
| 92a6ade7 |
export(
"getCoverage",
"expCoverage",
"contrCoverage",
|
| d059853f |
"getRawReads",
"expRawData",
"expRawData<-",
"contrRawData",
"contrRawData<-",
"getBatchRawReads",
|
| 92a6ade7 |
"getReadCountPerRestrictionFragment",
|
| d059853f |
"getBatchReadCountPerRestrictionFragment",
"getReadCountPerWindow",
"getBatchReadCountPerWindow",
|
| 92a6ade7 |
"getViewpoint",
"calculateRPM",
|
| d059853f |
"calculateBatchRPM",
"expReadCount",
"contrReadCount",
|
| 92a6ade7 |
"expRPM",
"contrRPM",
"getInteractions",
|
| d059853f |
"getBatchInteractions",
|
| 92a6ade7 |
"expInteractionRegions",
"contrInteractionRegions",
"plotOverviewInteractions",
"plotInteractionsNearViewpoint",
"plotInteractionsPerChromosome",
|
| d059853f |
"plotDomainogramNearViewpoint",
|
| 92a6ade7 |
"plot3Cecdf",
|
| d059853f |
"export3CseqRawReads2bedGraph",
|
| 92a6ade7 |
"export3Cseq2bedGraph",
"exportInteractions2text",
|
| d059853f |
"exportBatchInteractions2text",
"generate3CseqReport",
"getExpInteractionsInRefseq",
"getContrInteractionsInRefseq"
|
| 92a6ade7 |
)
|
