DSviaDRM: Exploring Disease Similarity in Terms of Dysfunctional Regulatory Mechanisms

Elucidation of human disease similarities has emerged as an active research area, which is highly relevant to etiology, disease classification, and drug repositioning. This package was designed and implemented for identifying disease similarities. It contains five functions which are 'DCEA', 'DCpathway', 'DS', 'comDCGL' and 'comDCGLplot'. In 'DCEA' function, differentially co-expressed genes and differentially co-expressed links are extracted from disease vs. health samples. Then 'DCpathway' function assigns differential co-expression values of pathways to be the average differential co-expression value of their component genes. Then 'DS' employs partial correlation coefficient of pathways as the disease similarity for each disease pairs. And 'DS' contains a permutation process for evaluating the statistical significant of observed disease partial correlation coefficients. At last, 'comDCGL' and 'comDCGLplot' sort out shared differentially co-expressed genes and differentially co-expressed links with regulation information and visualize them.

Author
Jing Yang
Date of publication
2015-05-12 11:45:13
Maintainer
Jing Yang <yangjing@scbit.org>
License
GPL (> 2)
Version
1.0

View on CRAN

Man pages

comDCGL
Sort out common DCGs and DCLs in multi-diseases
comDCGLplot
Visualization of common DCGs and DCLs
DCEA
Identify DCGs (Differentially Co-expressed Genes) and DCLs...
DCpathway
Calculate differential co-expression values (dCs) for each...
DS
Identification of disease similarity
DSviaDRM-package
Exploring disease similarity in terms of dysfunctional...
expressionBasedfilter
Filter genes according to expression level
exprs1
Real dataset pulled down from GEO...
exprs2
Real dataset pulled down from GEO...
exprs3
Real dataset pulled down from GEO...
pathways
The dataset of human pathways downloaded from two collections...
tf2target
The dataset of human Transcription Factors regulate potential...
varianceBasedfilter
To filter genes according to expression variability

Files in this package

DSviaDRM
DSviaDRM/NAMESPACE
DSviaDRM/data
DSviaDRM/data/exprs2.RData
DSviaDRM/data/exprs3.RData
DSviaDRM/data/pathways.RData
DSviaDRM/data/tf2target.RData
DSviaDRM/data/datalist
DSviaDRM/data/exprs1.RData
DSviaDRM/R
DSviaDRM/R/code20150507.r
DSviaDRM/MD5
DSviaDRM/DESCRIPTION
DSviaDRM/man
DSviaDRM/man/tf2target.Rd
DSviaDRM/man/pathways.Rd
DSviaDRM/man/exprs1.Rd
DSviaDRM/man/comDCGLplot.Rd
DSviaDRM/man/comDCGL.Rd
DSviaDRM/man/DCEA.Rd
DSviaDRM/man/expressionBasedfilter.Rd
DSviaDRM/man/DS.Rd
DSviaDRM/man/DSviaDRM-package.Rd
DSviaDRM/man/exprs3.Rd
DSviaDRM/man/DCpathway.Rd
DSviaDRM/man/exprs2.Rd
DSviaDRM/man/varianceBasedfilter.Rd