DeMixT_preprocessing: DeMixT_preprocessing

In wwylab/DeMixT: Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms

DeMixT_preprocessing

Description

DeMixT preprocessing in one go

Usage

DeMixT_preprocessing(
  count.matrix,
  normal.id,
  tumor.id,
  cutoff_normal_range = c(0.1, 1),
  cutoff_tumor_range = c(0, 2.5),
  cutoff_step = 0.2
)

Arguments

count.matrix	A matrix of raw expression count with G by (My + M1), where G is the number of genes, My is the number of mixed samples and M1 is the number of normal samples. Row names are genes column names are sample ids.
normal.id	A vector of normal sample ids
tumor.id	A vector of tumor sample ids
cutoff_normal_range	A vector of two numeric values, indicating the lower and upper bounds of standard deviation of log2 count matrix from the normal samples to subset. Default is c(0.2, 0.6)
cutoff_tumor_range	A vector of two numeric values, indicating the lower and upper bounds to search standard deviation of log2 count matrix from the normal samples to subset. Default is c(0.2, 0.6)
cutoff_step	A scatter value indicating the step size of changing cutoff_normal_range and cutoff_tumor_range to find a suitable subset of count matrix for downstream analysis

Value

processed count matrix

wwylab/DeMixT documentation built on July 13, 2024, 3:06 a.m.