A B C D E F G H I M N P R S X Y misc
as.list-method | Class 'HTClist' |
binningC | Windowing of high-throughput 'C' contact matrix |
c-method | Class 'HTCexp' |
c-method | Class 'HTClist' |
CQC | Quality Control for high-throughput 'C' experiment |
detail | Class 'HTCexp' |
detail-method | Class 'HTCexp' |
detail-method | Class 'HTClist' |
detail-methods | Class 'HTCexp' |
directionalityIndex | Directionality index calculation |
discretize | Transform matrix of counts data into discrete matrix |
divide | Class 'HTCexp' |
divide-method | Class 'HTCexp' |
divide-methods | Class 'HTCexp' |
E14 | HiTC - 5C data |
export-defunct | Class 'HTCexp' |
export.my5C | Export 'HTCexp' object to my5C website format |
exportC | Export 'HTCexp' object |
extractRegion | Extract a subset of the HTCexp object |
forcePairwise | Class 'HTClist' |
forcePairwise-method | Class 'HTClist' |
forceSymmetric-method | Class 'HTCexp' |
forceSymmetric-method | Class 'HTClist' |
forceTriangular | Class 'HTCexp' |
forceTriangular-method | Class 'HTCexp' |
getAnnotatedRestrictionSites | Annotation of restriction sites |
getCombinedContacts | Class 'HTClist' |
getCombinedContacts-method | Class 'HTClist' |
getCombinedIntervals | Class 'HTClist' |
getCombinedIntervals-method | Class 'HTClist' |
getExpectedCounts | Estimate expected interaction counts of a High-Throughput C intrachromsomal map based on the genomic distance between two loci |
getPearsonMap | Pearson correlation map |
getRestrictionFragmentsPerChromosome | Get a list of DNA restriction fragments |
HTCexp | Class 'HTCexp' |
HTCexp-class | Class 'HTCexp' |
HTClist | Class 'HTClist' |
HTClist-class | Class 'HTClist' |
id | Class 'HTCexp' |
id-method | Class 'HTCexp' |
id-methods | Class 'HTCexp' |
import.my5C | Import data from my5C webtool |
importC | Import high-htroughput 'C' data |
intdata | Class 'HTCexp' |
intdata-method | Class 'HTCexp' |
intdata<- | Class 'HTCexp' |
intdata<--method | Class 'HTCexp' |
intdata<--methods | Class 'HTCexp' |
intervalsDist | intervalsDist |
isBinned | Class 'HTCexp' |
isBinned-method | Class 'HTCexp' |
isBinned-method | Class 'HTClist' |
isBinned-methods | Class 'HTCexp' |
isComplete | Class 'HTClist' |
isComplete-method | Class 'HTClist' |
isComplete-methods | Class 'HTClist' |
isIntraChrom | Class 'HTCexp' |
isIntraChrom-method | Class 'HTCexp' |
isIntraChrom-method | Class 'HTClist' |
isIntraChrom-methods | Class 'HTCexp' |
isPairwise | Class 'HTClist' |
isPairwise-method | Class 'HTClist' |
isSymmetric | Class 'HTCexp' |
isSymmetric-method | Class 'HTCexp' |
isSymmetric-methods | Class 'HTCexp' |
isTriangular-method | Class 'HTCexp' |
isTriangular-methods | Class 'HTCexp' |
mapC | Visualize 'C' ontact map |
mapC-method | Visualize 'C' ontact map |
mapC-methods | Visualize 'C' ontact map |
MEF | HiTC - 5C data |
Nora_5C | HiTC - 5C data |
normICE | Iterative Correction of Hi-C data (ICE) |
normLGF | Local Genomic Feature (LGF) normalization |
normPerExpected | Class 'HTCexp' |
normPerExpected-method | Class 'HTCexp' |
normPerExpected-method | Class 'HTClist' |
normPerExpected-methods | Class 'HTCexp' |
normPerReads | Class 'HTCexp' |
normPerReads-method | Class 'HTCexp' |
normPerReads-methods | Class 'HTCexp' |
normPerTrans | Class 'HTCexp' |
normPerTrans-method | Class 'HTCexp' |
normPerTrans-methods | Class 'HTCexp' |
normPerZscore-defunct | Class 'HTCexp' |
pca.hic | Perform Principle Component Analysis on Hi-C contact map |
plot-method | Class 'HTCexp' |
plot-method | Class 'HTClist' |
range | Class 'HTCexp' |
range-method | Class 'HTCexp' |
range-method | Class 'HTClist' |
ranges | Class 'HTClist' |
ranges-method | Class 'HTClist' |
ranges-methods | Class 'HTClist' |
reduce | Class 'HTClist' |
reduce-method | Class 'HTClist' |
reduce-methods | Class 'HTClist' |
removeIntervals | Remove intervals from HTCexp object |
seqlevels | Class 'HTCexp' |
seqlevels-method | Class 'HTCexp' |
seqlevels-method | Class 'HTClist' |
seq_name-deprecated | Class 'HTCexp' |
setGenomicFeatures | Annotation of Hi-C contact map |
setIntervalScale | Set x and y interval of the HTCexp object |
show-method | Class 'HTCexp' |
show-method | Class 'HTClist' |
substract | Class 'HTCexp' |
substract-method | Class 'HTCexp' |
substract-methods | Class 'HTCexp' |
summary-method | Class 'HTCexp' |
summary-method | Class 'HTClist' |
xy_intervals | Class 'HTCexp' |
xy_intervals-method | Class 'HTCexp' |
xy_intervals-methods | Class 'HTCexp' |
x_intervals | Class 'HTCexp' |
x_intervals-method | Class 'HTCexp' |
x_intervals-methods | Class 'HTCexp' |
x_intervals<- | Class 'HTCexp' |
x_intervals<--method | Class 'HTCexp' |
x_intervals<--methods | Class 'HTCexp' |
y_intervals | Class 'HTCexp' |
y_intervals-method | Class 'HTCexp' |
y_intervals-methods | Class 'HTCexp' |
y_intervals<- | Class 'HTCexp' |
y_intervals<--method | Class 'HTCexp' |
y_intervals<--methods | Class 'HTCexp' |
[-method | Class 'HTClist' |