rowfisherMatVec: Perform Fisher Exact test between rows of mat (categorical)...
In nickytong/GenAnalysis: Genomic Analysis

Description Usage Arguments Value

This will perform fisher exact test; if this fails (e.g. due to large dimention or counts), chisq test will be used to get the result. Originally, ggplot2 figures are attached; this may takes a long time to cache the objects in knitr as well as saving it. Now ggplot2 objects are not computed and thus not returned to improve efficiency

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rowfisherMatVec(mat, vec, meta = list(tag = NULL, row = "group", response =
  "response"), more = TRUE, levels = NULL, parallel = FALSE, core = 1,
  addData = TRUE, ...)

`mat`	a matrix with rows as genes
`vec`	a factor giving the response
`meta`	meta information, a list. This can specify what type of analysis (i.e. KRAS vs NF1 mutation); row, which represents what row variables are (rows of mat); response represents what does OS mean
`more`	not implemented
`levels`	levels specified for the response vec; rows of mat are formatted with as.factor currently; (this is not tested if it controls levels for plotting although it does not affect p value calculation)
`core`	number of cores to use; this override parallel=TRUE if core=1 (no parallel)
`addData`	logical indicating if data (mat) should be attached as an attribute (may be used for scatter plot)
`...`	additional parameters to plotKM