scanStats: Run geneRxCluster scan statistics. Bioinformatics. 2014 Jun...

In everettJK/gt23: Gene therapy integration analysis tool suite.

Run geneRxCluster scan statistics. Bioinformatics. 2014 Jun 1;30(11):1493-500.

Description

Run geneRxCluster scan statistics. Bioinformatics. 2014 Jun 1;30(11):1493-500.

Usage

scanStats(gr1, gr2, gr1.label = "A", gr2.label = "B",
  kvals = "15L:30L", nperm = 100,
  cutpt.tail.expr = "critVal.target(k, n, target = 5, posdiff = x)",
  cutpt.filter.expr = "as.double(apply(x, 2, median, na.rm = TRUE))")

Arguments

kvals:

The interpretation of kvals = 2L:5L is that genomic windows will be drawn for every consecutive groups of integration sites with group sizes of 2, 3, 4, and 5 integration sites.

Value

Data frame of identified clusters with counts and statistics where target.min is the smallest nominal False Discoveries Expected for each cluster.

everettJK/gt23 documentation built on May 16, 2024, 12:04 p.m.