ORsurv: survival of patients using ors on TCGA data

Description Usage Arguments Value

View source: R/ORsurv.R

Description

survival of patients using ors on TCGA data

Usage

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ORsurv(
  folder,
  matrix_1,
  matrix_2,
  matrix_3,
  t1 = -3,
  t2 = 3,
  t3 = 3,
  name1 = "EXP",
  name2 = "EXP_TCGA",
  name3 = "Survival_plot",
  survival_info,
  method,
  month_limit,
  p_limit = 2,
  selected_label
)

Arguments

folder

dir name to save pdf files

matrix_1

zfpkm single sell matrix

matrix_2

tpm single cell matrix, same samples as in matrix_1

matrix_3

tpm bulk TCGA matrix

t1

cutoff for 0 and 1

t2

number of clusters on bianry matrix of single cell zfpkm

t3

number of clusters on projected matrix of single cells and bulk cells

name1

for binary matrix

name2

for projected matrix plots

name3

for survival plots

survival_info

for survival info

method

for pair-wise similarity method name

month_limit

keeping survival info till specfic months, means number of months

p_limit

therosld to selecte clusters where pair-wise p val is less

selected_label

to pass already known cluster names out of all clusters

Value

surv_plot pValues A vector containing FDR adjusted p significance values


krishan57gupta/ORsurv documentation built on Dec. 29, 2019, 4:56 p.m.