findMarkers: Derive signature matrices based on purified gene expression...

In lihuamei/LinDeconSeq: Cell Type Deconvolution using gene expression data for bulk samples.

Derive signature matrices based on purified gene expression profile.

Description

Derive signature marker genes by a series steps, including normalizing, filtered low confidence genes and DEG analysis.

Usage

findMarkers(
  refs,
  phes,
  QN = TRUE,
  q.cut = 0.01,
  p.cut = 0.1,
  opt.sigmat = TRUE,
  min.group = 50,
  max.group = 200,
  verbose = TRUE
)

Arguments

refs	Gene expression profile of each cell type, which rows represent genes and columns represent pure samples.
phes	Phenotype classes. Cell type (Row) x Sample name (column); value 1 = indicate membership of the reference sample; Otherwise, value = 0.
QN	Quantile normalization for expression profile or not, default: TRUE.
q.cut	Cutoff q-value for filtering candidate marker genes. default: 0.01.
p.cut	Cutoff p-value for assigning marker genes to cell type, default: 0.1.
min.group	Minimum number of each phnotype class when optimizing signature matrix, default: 50.
max.group	Maximum number of each phnotype class when optimizing signature matrix, default: 200.
verbose	logical, to print the detailed information.

Value

A list of derived results.

lihuamei/LinDeconSeq documentation built on Nov. 29, 2024, 2:59 p.m.