| Title: | Supporting data for package OMICsPCA |
|---|---|
| Description: | Supporting data for package OMICsPCA |
| Authors: | Subhadeep Das |
| Maintainer: | Subhadeep Das <[email protected]> |
| License: | GPL-3 |
| Version: | 1.30.0 |
| Built: | 2026-10-10 11:14:38 UTC |
| Source: | https://github.com/bioc/OMICsPCAdata |
a matrix containing cluster information
data("clustered_data")data("clustered_data")
The format is: num [1:300, 1:5] 3.37 -5.26 2.07 2.32 1.94 ... - attr(*, "dimnames")=List of 2 ..$ : chr [1:300] "ENST00000456433.1;ENST00000443722.1;ENST00000444457.1;ENST00000498530.1;ENST00000420236.2;ENST00000453466.1" "ENST00000423207.2" "ENST00000429514.2;ENST00000263893.6;ENST00000492639.1;ENST00000495272.1;ENST00000497058.1" "ENST00000487884.1" ... ..$ : chr [1:5] "Dim.1" "Dim.2" "Dim.3" "Dim.4" ...
data(clustered_data) ## maybe str(clustered_data) ; plot(clustered_data) ...data(clustered_data) ## maybe str(clustered_data) ; plot(clustered_data) ...
An output of create_group()
data("groupinfo_ext")data("groupinfo_ext")
A data frame with 28770 observations on the following variable.
groupa factor with levels IntE NE RE WE
data(groupinfo_ext) ## maybe str(groupinfo_ext) ; plot(groupinfo_ext) ...data(groupinfo_ext) ## maybe str(groupinfo_ext) ; plot(groupinfo_ext) ...
Histone modification ChIP-seq and CAGE data
data("multi_assay")data("multi_assay")
The datasets included in multi_assay are: 1) Histone modification ChIP-seq peaks of H2az, H3k9ac and H3k4me1. Each of these three datasets are in dataframe format, where the rows correspond to the TSSs and the columns correspond to various cell lines/tissues etc. Each value represents ChIP-seq peak intensity.
2) TSS expression data, measured by CAGE is also in data frame format and the row and column specification is same as the ChIP-seq data. Each value represents an normalized expression value (tpm).
The Histone modification are collected from : https://www.encodeproject.org/matrix/?type=Experiment&assay_title=ChIP-seq&target.investigated_as=broad+histone+mark The DNaseI hypersensitivity (DHS) datasests are collected from : http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/
The Histone fand DHS files are downloaded as bigbed(.bb) format and converted to bed(.bed) format
The CAGE datasets are collected from : https://www.encodeproject.org/search/?type=Experiment&assay_slims=Transcription&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&assay_title=CAGE
data(multi_assay) ## maybe str(multi_assay) ; plot(multi_assay) ...data(multi_assay) ## maybe str(multi_assay) ; plot(multi_assay) ...
details of GENCODE(v 17) TSSs
data("transcript_details")data("transcript_details")
A data frame with 194871 observations on the following 8 variables.
data(transcript_details) ## maybe str(transcript_details) ; plot(transcript_details) ...data(transcript_details) ## maybe str(transcript_details) ; plot(transcript_details) ...