getGeneData: Retieve Gene Expression and Factor Data

In ZachHunter/bvt: Visualization Tools for Bioconductor

Retieve Gene Expression and Factor Data

Description

Returns selected gene expression and factor data based on data type.

Usage

getGeneData(
  x,
  gene,
  plotType = "box",
  group = NULL,
  subgroup = NULL,
  highlight = NULL,
  facet = NULL,
  stack = NULL,
  symbol = "GeneSymbol",
  useNormCounts = TRUE,
  ...
)

Arguments

x	R data object; Most typically this is an ExpressionSet, but there is support for other data types as well.
gene	Gene name, row name of an expression table actualy vector/matrix of expression. In the case of gene names, the feature annotation element indicated by symbol is search for matches prior to checking the row names of the expression table (e.g. assayData).
plotType	character; Can be set to "box", "violin, "dot", "bar" or "density" for boxplots, violin plots, dot plots, bar plots, and kernal desity plots, respectively.
group	factor or name of factor to be exracted from x (e.g. pData). Used as the primary grouping factor.
subgroup	factor or name of factor to be exracted from x (e.g. pData). Used to subgroup data unless multiple genes are selected in which case subgroup is ignored.
highlight	factor or name of factor to be exracted from x (e.g. pData). Used to color data points by factor levels. Only valid for graphs with point overlays.
facet	factor or name of factor to be exracted from x (e.g. pData). Split the data into multiple smaller graphs.
stack	factor or name of factor to be exracted from x (e.g. pData). Used for stacked bar plots where both the individual and aggregate values are important. Valid only for bar plots.
symbol	character; Column name of of gene symbols in the feature data of x (e.g. fData).
useNormCounts	logical; By default genePlot will try to use normCounts instead of counts in SeqExpressionSets. Set to FALSE to use raw counts instead, though this will generate a warning about useing non-normalized data.
...	Any parameter recognized by NicePlots functions.

Details

These are a series of S3 methods that preprocess options based the data input type. Most Bioconductor data sets are supported. Once the pre-processing is complete, the generic version is called and for and the common pre-processing steps are performed prior to returning the data back to genePlot.

See Also

genePlot, ExpressionSet, SeqExpressionSet-class, EList-class, DESeqTransform

Examples

ToDo<-1

ZachHunter/bvt documentation built on Sept. 18, 2024, 3:12 p.m.