snv.predict: snv.predict

In mrrichowen/snv.predict: snv.predict uses true and false positives to improve snvs called from single cell RNA-seq data.

Description

This function predicts snvs in single cell RNA-seq data by creating a model based on true positives provided by the user and false positives from synthetic spike-ins (currently only ERCCs are supported). It will create a directory in the working directory called snv.predict.results containing a table of snv predictions.

Usage

snv.predict(nuseq_classifiers, truths)

Arguments

nuseq_classifiers	List of named data frames as output from nuseq-sc.
truths	List of named data.frames with snv information. Easiest to use the convenience function 'convert_to_pos' and add a fifth column with snvs annotated as true_positive (1), false_positive (0) and unknown (NA).

Examples

snv.predict(classifiers,truths)

mrrichowen/snv.predict documentation built on May 14, 2019, 5:27 p.m.