get_subgroup: Identify subgroup and control group for each clinical query...

In AllenSpike/CPDR: Cancer Drug Personalized Recommendation (CDPR)

Identify subgroup and control group for each clinical query sample

Description

Identify subgroup and control group for each clinical query sample

Usage

get_subgroup(
  cmat,
  mat,
  subtype,
  k = 10,
  biopsy = NULL,
  adjacent = FALSE,
  doplot = TRUE,
  OrgDB = NULL,
  db.path = tempdir()
)

Arguments

cmat	The RNA-seq count expression profiles of clinical query samples.
mat	Profiles of selected TCGA data set.
subtype	The NMF subtyping result.
k	The subgroup size (10 by default. Optional 3, 5, 10.)
biopsy	Tissue sources of the control group (Use View(GTEX_set) for optional 51 biopsy.sites. By default set to NULL, which will select control group based on distance between TCGA and GTEX samples.)
adjacent	A logical value. By default set to FALSE. If TRUE, only tissue with sample.type 'adjacent' from GTEX_set would be used instead of 'normal'.
doplot	A logical value. If TRUE, draw the heatmap of Spearman correlation coefficients between query samples and subtypes.
db.path	A character(1) string with the folder path where the background data was saved.
OrgDb	The human annotation db for ID convert.

Value

Profiles of subgoups and control groups for each clinical query sample.

AllenSpike/CPDR documentation built on April 18, 2022, 4:38 p.m.