Find Isoform Switching Events
Usage
switch_calculator(
cancer_ori,
gtex_ori,
exp_values_pcawg,
exp_values_gtex,
ensp_sequences,
cutoff,
cutoff_rate,
cutoff_other_MDTs,
ensp_only
)Arguments
- cancer_ori
MDT files of cancer cohort
- gtex_ori
MDT files of normal cohort
- exp_values_pcawg
abundance dataframe of cancer samples
- exp_values_gtex
abundance dataframe of gtex samples
- ensp_sequences
ensp sequences of transcripts
- cutoff
cutoff
- cutoff_rate
enrichment value (for example MDT1 should be expressed >=2 than the next one)
- cutoff_other_MDTs
cutoff to decide percentage of MDTs found in normal samples
- ensp_only
transcripts having ENSP ids