A subset of the TCGA lung squamous cell carcinoma (LUSC) gene expression dataset. It contains the first 50 primary tumor samples, pre-processed to log2(TPM + 1) values. This dataset is used for code examples and the package vignette.
Usage
data(TCGA_LUSC)Format
A numeric matrix with 22,962 rows (genes) and 50 columns (samples):
- rownames
Official gene symbols (e.g., TP53, KRAS).
- colnames
TCGA sample barcodes (e.g., TCGA-XX-XXXX-01A).
Details
The original TPM values were normalized and then log2-transformed using
log2(x + 1) to stabilize variance. The subset was created by selecting
the first 22,962 rows and 50 columns from the full processed matrix to
keep the package size small. All samples correspond to primary tumor
tissue (sample type code '01').
Because the data are already log2-transformed, they will pass the
internal log2 check in classifyHNSC() and will not be re-transformed.
Examples
data(TCGA_LUSC)
# Check dimensions
dim(TCGA_LUSC)
#> [1] 22962 50
# First few genes and samples
TCGA_LUSC[1:5, 1:3]
#> TCGA-18-3406-01A TCGA-18-3407-01A TCGA-18-3408-01A
#> A1BG 0.09868904 0.022048165 0.1824381
#> A1BG-AS1 0.86568131 0.560323662 0.1108977
#> A1CF 0.05018822 0.009203827 0.0000000
#> A2M 6.58947438 7.875843327 8.4736161
#> A2M-AS1 0.58428909 0.645332754 1.8565077