1. Download the gene expression file (e.g. CCLE_RNAseq_genes_rpkm_20180929.gct) from CCLE
2. Classify samples into the highest quarter group (labeled as 0 in exp_group.txt) and the lowest quarter group (labeled as 1 in exp_group.txt) according to expression levels of one specific gene
./group.py checked_gene gene_list.txt CCLE_RNAseq_genes_rpkm_20180929.gct > exp_group.txt
- input:
- checked_gene: gene symbol used to classify groups (e.g. LIG3)
- gene_list.txt: list of tested genes
- CCLE_RNAseq_genes_rpkm_20180929.gct: gene expression file
- output:
- exp_group.txt: gene_symbol group_label expression_level
./plot.R exp_group.txt boxplots.pdf