surv_cox {tinyarray}

surv_cox

Description

calculate cox p values and HR for genes

Usage

surv_cox(
  exprSet_hub,
  meta,
  cut.point = FALSE,
  pvalue_cutoff = 0.05,
  HRkeep = "all",
  continuous = FALSE,
  min_gn = 0.1
)

Arguments

exprSet_hub

a tumor expression set for hubgenes

meta

meta data corresponds to expression set

cut.point

logical , use cut_point or not, if FALSE,use median by defult

pvalue_cutoff

p value cut off ,0.05 by defult

HRkeep

one of "all","protect"or"risk"

continuous

logical, gene expression or gene expression group

min_gn

Depending on the expression of a gene, there may be a large difference in the number of samples between the two groups, and if a smaller group of samples is less than 10 percent (default) of all, the gene will be discarded

Value

a matrix with gene names ,cox p value and HR

Author(s)

Xiaojie Sun

See Also

point_cut;surv_KM

Examples

surv_cox(exprSet_hub1,meta1)
surv_cox(exprSet_hub1,meta1,cut.point = TRUE,continuous = TRUE)
surv_cox(exprSet_hub1,meta1,cut.point = TRUE,continuous = TRUE,pvalue_cutoff = 1)