Nora_5C: HiTC - 5C data

In HiTC: High Throughput Chromosome Conformation Capture analysis

Description

5C data described by Nora et al. (2012)

Usage

data(Nora_5C)

Format

Contains two HTClist objects (E14 and MEF). Each of them containing the ChrX intrachromosomal maps as a HTCexp object.

Details

This 5C dataset published by Nora et al (GSE35721), contains two different samples, a male undifferentiated ES cells (E14, GSM873935) and a mouse embryonic fibroblasts (MEF, GSM873924). This dataset is mainly used to describe the available functionalities of the HiTC package. The data provided with the package are count data.

Source

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE35721

References

Nora EP, Lajoie BR, Schulz EG, Giorgetti L et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 2012 Apr 11;485(7398):381-5. PMID: 22495304

Examples

data(Nora_5C)
show(E14)
show(MEF)

Example output

Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
HTClist object of length 1 
1 intra / 0 inter-chromosomal maps
HTClist object of length 1 
1 intra / 0 inter-chromosomal maps

HiTC documentation built on Nov. 8, 2020, 8:27 p.m.