|
Please see the DESCRIPTION file.
● Data Source:
BioConductor
● Keywords:
● Alias: DMRforPairs-package
●
0 images
|
DMRforPairs
(Package: DMRforPairs) :
WRAPPER FOR THE DMRforPairs ANALSYSIS
Wrapper for the DMRforPairs analysis. Includes recoding of the probe classes, identification of sufficiently probe-dense regions and analysis (calculation of statistics and testing).
● Data Source:
BioConductor
● Keywords: analysis
● Alias: DMRforPairs
●
0 images
|
calc_stats
(Package: DMRforPairs) :
CALCULATE DESCRIPTIVE AND TEST STATISTICS
Calculate the (difference in) median beta and M values for the rows specified in probe_rows (descriptive statistics). probe_rows must specify a continuous range of adjacent probes. If a regions shows an high difference (>dM_min) between any pair of samples, the differences are formally tested (Mann Whitney U if n=2, Kruskal Wallis n>2). If n>2 and the omnibus test is significant , pairwise testing is performed to determine which differ significantly.
● Data Source:
BioConductor
● Keywords: analysis
● Alias: calc_stats
●
0 images
|
export_data
(Package: DMRforPairs) :
COMPLETE EXPORT AND VISUALIZATION OF DMRforPairs RESULTS
Complete export of the DMRforPairs results. Export includes pdf's, thumbnails and TSV files describing the methylation status of all relevant (median delta M > dM_min) regions. M and beta values plotted against genomic position. Plots are generated for all samples and sample pairs (if n>2). Annotation information can be automatically looked up in the Ensembl database. If this is requested, integrated figures of the methylation pattern are generated including all transcripts annotated to the region of interest (+margin). This function also generates overviews (tables) in tsv and HTML format with information about the regions and their methylation status in the samples. This is done separately for all regions, regions with a relevant difference and regions with a significant difference.
● Data Source:
BioConductor
● Keywords: export_visualization
● Alias: export_data
●
0 images
|
|
Illumina assigns quite specific functional classes to the probes. 11 classes are defined (Bibikova et al. 2009 & 2011):
● Data Source:
BioConductor
● Keywords: analysis
● Alias: merge_classes
●
0 images
|
Wrapper for plot_annotate_probes. Generates a plot of the methylation status of a custom genomic region.
● Data Source:
BioConductor
● Keywords: export_visualization
● Alias: plot_annotate_custom_region
●
0 images
|
Wrapper for plot_annotate_probes. Generates a plot of the methylation status of / around a specific gene.
● Data Source:
BioConductor
● Keywords: export_visualization
● Alias: plot_annotate_gene
●
0 images
|
|
Function that visualizes the methylation status of a selection of adjacent probes and (if requested) identifies transcripts associated with that region. If n>2 plots are generated for all samples together as well as in a pairwise fashion.
● Data Source:
BioConductor
● Keywords: export_visualization
● Alias: plot_annotate_probes
●
0 images
|
Wrapper for plot_annotate_probes. Generates a plot of the methylation status of a region identified by DMRforPairs and associated transcripts (if annotate=TRUE).
● Data Source:
BioConductor
● Keywords: export_visualization
● Alias: plot_annotate_region
●
0 images
|
regionfinder
(Package: DMRforPairs) :
IDENTIFICATION OF PROBE DENSE REGIONS
Identifies genomic regions with sufficient probe density, i.e. a high number of probes positioned closely together.
● Data Source:
BioConductor
● Keywords: analysis
● Alias: regionfinder
●
0 images
|
providing 
.