getPvalue: Returning only the p values
In brightchan/cjbmisc:

A group of functions to return only the p values from various of tests.

p_fish.chi.t: Try first use fish.t to get p value,
if failed (usually due to too many catergories), then use chisq.t with popup warning.
If only Fisher's exact test or ChiSQ is wanted, specify it in "p.test" parameter
p_aov.t: p-value from aov
p_ContDisc: p-value from t.test,wilcox.test,kruskal.test
p_ContCont: p-value from cor.test or fromp_lm
p_lm: p-value of the coefficient from the univariate lm
p_adjust_mat: adjust a matrix of p-values
p_xVsAll: generate a vector of pvalues by contrasting x vs all the rest of the variables in a dataframe.
p_dfAll: generate a df of pvalues by contrasting all x.coln vs all y.coln. parameters are the same as in p_xVsAll
p_uniCox: generate a list of univariate Cox models and a vector of the minimal pvalue from each model
p_feat_subtype: p-value of a set of features according to a subtype in a manner similar to plot_feat_subtype

p_fish.chi.t(df, v1, v2, alt = "two.sided", p.test = "both", ws = 2e+06)

p_aov.t(df, v1, v2)

p_ContCont(df, v1, v2, method = "spearman")

p_ContDisc(df, v1, v2, method = "kruskal.test")

p_lm(df, v1, v2)

p_xVsAll(
  df,
  x.coln,
  y.coln = NULL,
  num.num.test = "spearman",
  cat.num.test = "kruskal.test",
  cat.cat.test = "both"
)

p_dfAll(df, x.coln, y.coln = NULL, ...)

p_uniCox(
  survdf,
  feat,
  surv.time = "PFS.days",
  surv.status = "PFS.status",
  signif.cutoff = 0.05,
  keep.all.in.barplot = F,
  plot.surv = T,
  survp.xlim = c(0, 1400),
  survp.timebreak = 365
)

p_adjust_mat(pvaldf, p.adjust.method = "BH")

`df`	dataframe with rows of samples and columns of features, one column should contain the subtype info.
`v1, v2`	character of the column name in the df
`alt`	passing to alternative in `fisher.test`, should be one of "two.sided", "greater" or "less". You can specify just the initial letter. Only used in the 2 by 2 case.
`p.test`	Should be "fisher" or "chi", to use only that method to get p values.
`ws`	passing to workspace size in `fisher.test`, integer specifying the size of the workspace used in the network algorithm. In units of 4 bytes.
`method`	p_ContDisc: the test method to-be-used, can be t.test, kruskal.test or wilcox.test
`...`	for p_feat_subtype, pass to `p_fish.chi.t`
`feat`	character vector of the features to be calculated
`subtype`	column name of the subtype
`cont.test`	the significance test to be used for continuous variables. Use the name of the r basic tests.
`disc.test`	the significance test to be used for discrete variables. Should be "fisher","chi" or"both"