BIGEE: BIGEE: Bimodal Gene Expression Exclusivity.
In BiSEp: Toolkit to Identify Candidate Synthetic Lethality

Description Usage Arguments Details Value Author(s)

Part of the Synthetic Lethality detection in Genomics toolkit. Detects bimodality and non-normality in all genes across the dataset. Compares all pairwise combinations of bimodal genes and searches for mutually exclusive low expression as evidence of potential synthetic lethality. Scores gene-pairs based on the presence of mutual exclusive bimodality and the distribution of signal intensity across the rest of the dataset.

BIGEE(
	bisepData=data, 
	sampleType=c("cell_line", "cell_line_low", "patient", "patient_low")
	)

`bisepData`	This should be the output from the BISEP function.
`sampleType`	The type of sample being analysed. Select 'cell_line' or 'patient' for datasets with greater than ~200 samples. For datasets with less than ~200 samples, use 'cell_line_low' or 'patient_low'.

Lower sample numbers have more stringent bimodality hurdles to clear in order to keep the false positive rate lower. The tool returns a percentage complete text window so the user can observe the status of the job.

A matrix containing three columns. Columns 1 and 2 are the gene symbols that make up the candidate synthetic lethal gene pairs. Column 3 is the score calculated the tool to rank the statistical significance of the gene pairs.

Mark Wappett

BiSEp documentation built on May 2, 2019, 9:13 a.m.