High Throughput Chromosome Conformation Capture analysis

[Up] [Top]

Documentation for package ‘HiTC’ version 1.2.0

Help Pages

binningC Windowing of high-throughput 'C' interaction matrix
CQC Quality Control for high-throughput 'C' experiment
detail Class 'HTCexp'
detail-method Class 'HTCexp'
detail-methods Class 'HTCexp'
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 Class 'HTCexp'
export-method Class 'HTCexp'
export-methods Class 'HTCexp'
export.my5C Export 'HTCexp' object to my5C website format
exportC Export 'HTCexp' object
extractRegion Extract a subset of the HTCexp object
getExpectedCounts Estimate expected interaction counts of a High-Throughput C intrachromsomal map based on the genomic distance between two loci
HTCexp Class 'HTCexp'
HTCexp-class Class 'HTCexp'
id Class 'HTCexp'
id-method Class 'HTCexp'
id-methods Class 'HTCexp'
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-methods Class 'HTCexp'
intdata<- Class 'HTCexp'
intdata<--method Class 'HTCexp'
intdata<--methods Class 'HTCexp'
intervalsDist intervalsDist
isBinned Class 'HTCexp'
isBinned-method Class 'HTCexp'
isBinned-methods Class 'HTCexp'
isIntraChrom Class 'HTCexp'
isIntraChrom-method Class 'HTCexp'
isIntraChrom-methods Class 'HTCexp'
mapC Visualize 'C' interaction map
MEF HiTC - 5C data
Nora_5C HiTC - 5C data
normPerExpected Class 'HTCexp'
normPerExpected-method Class 'HTCexp'
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 Class 'HTCexp'
normPerZscore-method Class 'HTCexp'
normPerZscore-methods Class 'HTCexp'
plot Class 'HTCexp'
plot-method Class 'HTCexp'
plot-methods Class 'HTCexp'
range Class 'HTCexp'
range-method Class 'HTCexp'
range-methods Class 'HTCexp'
readBED readBED
removeIntervals Remove intervals from HTC object
seq_name Class 'HTCexp'
seq_name-method Class 'HTCexp'
seq_name-methods Class 'HTCexp'
setIntervalScale Set x and y interval of the HTCexp object
show Class 'HTCexp'
show-method Class 'HTCexp'
show-methods Class 'HTCexp'
substract Class 'HTCexp'
substract-method Class 'HTCexp'
substract-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'