proc_colon {bspcov} | R Documentation |
Preprocess Colon Gene Expression Data
Description
The proc_colon
function preprocesses colon gene expression data by:
Log transforming the raw counts.
Performing two-sample t-tests for each gene between normal and tumor samples.
Selecting the top 50 genes by absolute t-statistic.
Returning the filtered expression matrix and sample indices/groups.
Usage
proc_colon(colon, tissues)
Arguments
colon |
A numeric matrix of raw colon gene expression values (genes × samples). Rows are genes; columns are samples. |
tissues |
A numeric vector indicating tissue type per sample: positive for normal, negative for tumor. |
Value
A list with components:
- X
A numeric matrix (samples x 50 genes) of selected, log‐transformed expression values.
- normal_idx
Integer indices of normal‐tissue columns in the original data.
- tumor_idx
Integer indices of tumor‐tissue columns in the original data.
- group
Integer vector of length
ncol(colon)
, with 1 = normal, 2 = tumor.
Examples
data("colon")
data("tissues")
set.seed(1234)
colon_data <- proc_colon(colon, tissues)
X <- colon_data$X
foo <- bmspcov(X, Sigma = cov(X))
sigmah <- estimate(foo)