rowkmMatVec: Perform log rank test between rows of mat (categorical) and a...

In nickytong/GenAnalysis: Genomic Analysis

Description

Notice that ggplot2 figures are attached; this may takes a long time to cache the objects in knitr

Usage

rowkmMatVec(mat, OS, OScensoring, meta = list(tag = NULL, row = "group",
  response = "Overal survival"), more = TRUE, levels = NULL,
  parallel = FALSE, core = 1, addData = TRUE, ...)

Arguments

mat	a matrix with rows as genes
OS	a vector giving the survival time. This can be for example overall survival, PFS and others
OScensoring	a vector giving the censor status. 1 is event and 0 is censored.
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 each row of mat
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

Value

a rowkmMatVec class; meta information is stored as attributes

nickytong/GenAnalysis documentation built on July 20, 2019, 8:57 a.m.