getWriteHeatmap: Write DE genes from contrasts, return DE genes and plot...

In peterjuv/FunGenPipe: Tools for building function genomics pipelines

Description

File names correpond to names from fits dot(.) names from contrasts

Usage

getWriteHeatmap_probesTTcontrasts(
  outPath,
  esets,
  fits,
  contMatrices,
  pVals,
  varColSideColors,
  targetsOrder = NULL,
  pValDE = 0.05,
  maxHeatMapProbes = 50
)

getWriteHeatmap_probesTTcomparisons(
  outPath,
  esets,
  fits,
  comparisons,
  pVals,
  varColSideColors,
  targetsOrder = NULL,
  pValDE = 0.05,
  maxHeatMapProbes = 50
)

getWriteHeatmap_PgseaTTcontrasts(
  outPath,
  gscPGSEA,
  esetsPGSEA,
  fitsPGSEA,
  contMatrices,
  useNameCol,
  fitsProbes,
  esetsProbes,
  pVals,
  varColSideColors,
  targetsOrder = NULL,
  pValDE = 0.05,
  maxHeatMapProbes = 50,
  setIDCol = NULL
)

getWriteHeatmap_PgseaTTcomparisons(
  outPath,
  gscPGSEA,
  esetsPGSEA,
  fitsPGSEA,
  comparisons,
  useNameCol,
  fitsProbes,
  esetsProbes,
  pVals,
  varColSideColors,
  targetsOrder = NULL,
  pValDE = 0.05,
  maxHeatMapProbes = 50,
  setIDCol = NULL
)

Arguments

outPath	Path to write TTs
esets	Named list of esets for BiocGenerics::annotation of probes with columns PROBEID, SYMBOL, ENTREZID, HSA_ENTREZID
fits	Named list of PGSEA fits
contMatrices	Named list of contrast matrices with Levels & Contrasts
pVals	Numeric vector p-values for heatmaps
varColSideColors	String variable name from pData(esets[.]) (i.e. targets) with an associated "color_<varColSideColors>"
targetsOrder	Order of samples, used for plotting heatmaps w/o clustering of samples; default NA
pValDE	Numeric p-value for DEG, default 0.05
maxHeatMapProbes	Numeric max number of DEG for heatmaps, default 50
comparisons	Named list of comparisons made from names of contrasts
gscPGSEA	Named list of gene set collection
esetsPGSEA	Named list of PGSEA esets
fitsPGSEA	Named list of PGSEA fits
useNameCol	Name of the column from Biobase::fData(esetsPGSEA[?]) to show with heatmaps
fitsProbes	Named list of probe fits
esetsProbes	Named list of esets for BiocGenerics::annotation of probes with columns PROBEID, SYMBOL, ENTREZID, HSA_ENTREZID
setIDCol	Character column name with rownames (i.e. IDs of gene sets) added to limma::topTable; default NULL

Value

Named list of limma::topTable() results (TTs) of DE genes / enriched sets; names corresponds to names of fits

Functions

• getWriteHeatmap_probesTTcontrasts: Write DE genes from contrasts, return DE genes and plot heatmaps

• getWriteHeatmap_probesTTcomparisons: Write DE genes from comparisons, return DE genes and plot heatmaps

• getWriteHeatmap_PgseaTTcontrasts: Write enriched pathways from contrasts, return patways and plot heatmaps

• getWriteHeatmap_PgseaTTcomparisons: Write enriched pathways from comparisons, return patways and plot heatmaps

Examples

## Not run: 
getWriteHeatmap_PgseaTTcontrasts(outPath=file.path(resultDirOut, "3.PGSEA.KEGGREST.limma-contrasts"), gscPGSEA=gscKeggrestHsa, 
  esetsPGSEA=esetsKeggrest, fitsPGSEA=fitsKeggrest, useNameCol="keggPathNameHsa2", fitsProbes=fits, esetsProbes=esets, pVals)
getWriteHeatmap_PgseaTTcontrasts(file.path(resultDirOut, "3.PGSEA.TRANSFAC.2016.1.byFA.limma-contrasts"), gscTF.facFA, 
  esetsTF.facFA, fitsTF.facFA, useNameCol="factorFA", fits, esets, pVals)

## End(Not run)
## Not run: 
writeHeatmap_PgseaTTcomparisons(outPath=file.path(resultDirOut, "3.PGSEA.KEGGREST.limma-comparisons"), gscPGSEA=gscKeggrestHsa,
  esetsPGSEA=esetsKeggrest, fitsPGSEA=fitsKeggrest, comparisons=comparisons, useNameCol="keggPathNameHsa2", fitsProbes=fits, 
  esetsProbes=esets, pVals=pVals, varColSideColors="SexFs", targetsOrder=targetsOrder, setIDCol="KeggID")

## End(Not run)

peterjuv/FunGenPipe documentation built on June 18, 2021, 3:38 a.m.