getIsoData: Extract Isoform Expression Data

In ZachHunter/bvt: Visualization Tools for Bioconductor

Extract Isoform Expression Data

Description

Preprocess Isoform expression data for downstream analysis and plotting.

Usage

getIsoData(
  d,
  isoforms = NULL,
  plotType = plotType,
  group = NULL,
  subgroup = NULL,
  highlight = NULL,
  facet = NULL,
  stack = NULL,
  useNormCounts = TRUE,
  appris = NULL,
  transcriptType = NULL,
  symbol = "GeneSymbol",
  ttype = "transcript_type",
  ...
)

Arguments

d	R data object with stored isoform annotation data; Most typically this is an ExpressionSet there is support for other datatypes as well.
isoforms	character; A vector of isoform IDs to include in the output. Can be used in combination with with genes.
plotType	character; Can be set to "box", "violin, "dot", "bar" or "denisity" 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.
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.
appris	boolean or character; If set to TRUE, will return only isoforms with appris annotation. If set to a character string, will restirct isoforms to those with the character value matching a substring of the appris tag. Appris collumn is determined by the first collumn name to containing 'Appris' (case insenstive).
transcriptType	character; Returns only those isoforms where the transcript type collumn has a substring that matches the character value supplied such as 'protein' in 'protein_coding'. The transcript type collumn is determined by the ttype option.
symbol	character; Column name of the optional gene symbols column in the annotation. The default value is 'GeneSymbol'.
ttype	character; Column name of the optional transcript type column in the annotation. The default value is 'transcript_type'.
...	additional parameters for S3 variants.

Details

ToDO

Value

ToDo

See Also

isoPlot showIsoforms getGeneData

Examples

ToDo<-1

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