LncDM: The Different Methylation Sites, Elements and Regions of lncRNA

The package can get the methylation matrix and identify the differential methylation sites,elements or the regions who are in the elements of lncRNA etc. This package gets a matrix of methylation values of the samples. Then it can calculate the methylation values of elements. This package uses linear and t test to identify the differential methylation or the sites,elements and regions that related with the phenotype.

Author
Hui Zhi,Yanxun Su,Xin Li
Date of publication
2016-07-22 01:39:57
Maintainer
Hui Zhi<zhihui013201@gmail.com>
License
GPL-2
Version
1.0

View on R-Forge

Man pages

dme
Find the differential methylation elements of lincRNA,...
dmr
Find the differential methylation regions in the elements of...
dms
Find the differential methylation CpG sites in the lincRNA,...
loaddata
Load and preprocessed raw data
regionLevel
Calculate the beta values of elements in lincRNA etc

Files in this package

LncDM/DESCRIPTION
LncDM/NAMESPACE
LncDM/R
LncDM/R/dme.R
LncDM/R/dmr.R
LncDM/R/dms.R
LncDM/R/loaddata.R
LncDM/R/regionLevel.R
LncDM/build
LncDM/build/vignette.rds
LncDM/inst
LncDM/inst/doc
LncDM/inst/doc/LncDM.R
LncDM/inst/doc/LncDM.Rnw
LncDM/inst/doc/LncDM.pdf
LncDM/inst/extdata
LncDM/inst/extdata/annotation
LncDM/inst/extdata/annotation/CpGannotation.Rdata
LncDM/inst/extdata/annotation/annotation.Rdata
LncDM/inst/extdata/annotation/dmrAnno.Rdata
LncDM/inst/extdata/localdata
LncDM/inst/extdata/localdata/BRCA_pheno.txt
LncDM/inst/extdata/localdata/Level_2
LncDM/inst/extdata/localdata/Level_2/TCGA-3C-AAAU-01A-11D-A41Q-05.txt
LncDM/inst/extdata/localdata/Level_2/TCGA-3C-AALI-01A-11D-A41Q-05.txt
LncDM/inst/extdata/localdata/Level_2/TCGA-3C-AALJ-01A-31D-A41Q-05.txt
LncDM/inst/extdata/localdata/Level_2/TCGA-BH-A1F0-11B-23D-A138-05.txt
LncDM/inst/extdata/localdata/Level_2/TCGA-E2-A15I-11A-32D-A138-05.txt
LncDM/inst/extdata/localdata/loadData.Rdata
LncDM/man
LncDM/man/dme.Rd
LncDM/man/dmr.Rd
LncDM/man/dms.Rd
LncDM/man/loaddata.Rd
LncDM/man/regionLevel.Rd
LncDM/vignettes
LncDM/vignettes/LncDM.Rnw
LncDM/vignettes/Manhattan.png
LncDM/vignettes/density-plot1.png
LncDM/vignettes/density-plot2.png
LncDM/vignettes/density-plot3.png
LncDM/vignettes/detect-pvalue.png
LncDM/vignettes/dmr-boxplot.png
LncDM/vignettes/dms-boxplot.png
LncDM/vignettes/heatmap-of-CpG-sites1.png
LncDM/vignettes/heatmap-of-CpG-sites2.png
LncDM/vignettes/heatmap-of-DMR.png
LncDM/vignettes/heatmap-of-DMS.png
LncDM/vignettes/lincRNARegion1.png
LncDM/vignettes/lincRNARegion2.png
LncDM/vignettes/lincRNA_plot1.png
LncDM/vignettes/lincRNA_plot2.png