imr90.1.obs: A non-corrected CIM of replicate 1 of IMR90, for chromosomes...

In chromoR: Analysis of chromosomal interactions data (correction, segmentation and comparison)

Description

A non corrected chromosomal interaction map (CIM) for replicate 1 of IMR90, for chromosomes 1 and 2, generated from a publicly available Hi-C data set [1]. This matrix was build with BuildCIM given Hi-C mapped positions, publicly available

from http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE35156

Usage

data(imr90.1.obs)

Format

A matrix

References

[1] J. R. Dixon, S. Selvaraj, F. Yue, A. Kim, Y. Li, Y. Shen, M. Hu, J. S. Liu and B. Ren, Nature, 2012, 485, 376.

See also http://www.cl.cam.ac.uk/~ys388/chromoR/ for the genome wide CIM.

Examples

data(imr90.1.obs)

Example output

Loading required package: haarfisz
Loading required package: wavethresh
Loading required package: MASS
WaveThresh: R wavelet software, release 4.6.8, installed

Copyright Guy Nason and others 1993-2016

Note: nlevels has been renamed to nlevelsWT

Loading required package: gdata
sh: 1: cannot create /dev/null: Permission denied
gdata: Unable to locate valid perl interpreter
gdata: 
gdata: read.xls() will be unable to read Excel XLS and XLSX files
gdata: unless the 'perl=' argument is used to specify the location of a
gdata: valid perl intrpreter.
gdata: 
gdata: (To avoid display of this message in the future, please ensure
gdata: perl is installed and available on the executable search path.)
sh: 1: cannot create /dev/null: Permission denied
gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLX' (Excel 97-2004) files.

gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.

gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.

Attaching package: 'gdata'

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

    nobs

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

    object.size

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

    startsWith

chromoR documentation built on May 2, 2019, 2:05 p.m.