surv_cox function

surv_cox

calculate cox p values and HR for genes

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

Returns

a matrix with gene names ,cox p value and HR

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)

See Also

point_cut;surv_KM

Author(s)

Xiaojie Sun