R Graphical Manual

Last data update: 2014.03.03

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Results 1 - 10 of 14 found.
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DisplayName (Package: rgsepd) :

Convert a NM## id number to the corresponding HGNC Gene name, where available.

● Data Source: BioConductor
● Keywords:
● Alias: DisplayName
● 0 images

GSEPD_ChangeConditions (Package: rgsepd) : GSEPD_ChangeConditions

This function is an interface to set which samples are the test conditions. Don't forget to GSEPD_Process() after changing settings. If you want to systematically try each condition pairing, try GSEPD_ProcessAll()

● Data Source: BioConductor
● Keywords:
● Alias: GSEPD_ChangeConditions
● 0 images

GSEPD_ChangeOutput (Package: rgsepd) : GSEPD_ChangeOutput

Update the stored output folder designation, and create it if necessary. This is useful if you want to change some LIMIT parameters and re-run the pipeline. Don't forget to GSEPD_Process() after changing settings.

● Data Source: BioConductor
● Keywords:
● Alias: GSEPD_ChangeOutput
● 0 images

GSEPD_DEGHeatmap (Package: rgsepd) :

Generates a gene-by-subject heatmap plot of differentially expressed genes.

● Data Source: BioConductor
● Keywords: plot
● Alias: GSEPD_DEGHeatmap
● 0 images

GSEPD_Export_DESeq (Package: rgsepd) :

Converts from the internal matrices to a DESeq standard object.

● Data Source: BioConductor
● Keywords: DESeq2
● Alias: GSEPD_Export_DESeq
● 0 images

GSEPD_Heatmap (Package: rgsepd) :

Plots the heatmap to the standard display. Uses heatmap.2 from gplots to display selected genes' expression level.

● Data Source: BioConductor
● Keywords: heatmap, plot
● Alias: GSEPD_Heatmap
● 1 images

GSEPD_INIT (Package: rgsepd) :

Initializes the system, here you will pass in the count dataset and the sample metadata, before any GSEPD processing. Return value is a named list holding configurable parameters.

● Data Source: BioConductor
● Keywords:
● Alias: GSEPD_INIT
● 0 images

GSEPD_PCA_Plot (Package: rgsepd) : Principle Components Analysis figure generation

After processing the pipeline, users may want to have further PCA figures generated. This function takes a completed GSEPD object and generates informative figures, based on the differentially expressed genes.

● Data Source: BioConductor
● Keywords:
● Alias: GSEPD_PCA_Plot
● 0 images

GSEPD_PCA_Spec (Package: rgsepd) : Specialized PCA Plot

After processing the pipeline, users may want to have further PCA figures generated. This function takes a completed GSEPD object and generates informative figures. This function includes parameters to specify a particular GO-Term of interest.

● Data Source: BioConductor
● Keywords:
● Alias: GSEPD_PCA_Spec
● 1 images

GSEPD_Process (Package: rgsepd) :

Primary interface, use this function to kick off the pipeline.

● Data Source: BioConductor
● Keywords:
● Alias: GSEPD_Process
● 0 images