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.

AuthorHui Zhi,Yanxun Su,Xin Li
Bioconductor views DMR LncRNA Methylation Statistics
Date of publication2016-07-22 01:39:57
MaintainerHui Zhi<zhihui013201@gmail.com>
LicenseGPL-2
Version1.0

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Files

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

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