PCG PCA¶
PCG analysis in PCG PC space
usage¶
python3 pca.py -h
argument |
description |
|---|---|
-h, –help |
show this help message and exit |
–name NAME, -n NAME |
sample name |
–symbol SYMBOL, -s SYMBOL |
symbol |
–trainingData TRAININGDATA, -t TRAININGDATA |
training dataset, cols are genes, rows are bins |
–pcg PCG, -p PCG |
known pcg list file |
–genes GENES, -g GENES |
target gene list file |
–classes CLASSES, -c CLASSES |
pcg class file |
–data DATA, -i DATA |
data expression file to project in PC space, cols are genes, rows are bins |
example¶
python3 pca.py -i total.csv -t WT.csv -p pcg.txt -c pcg_class.txt -n test_WT
python3 pca.py -i total.csv -t WT.csv -g filtered_gene.txt -p pcg.txt -c pcg_class.txt -n test_WT -s symbols.txt