tbt_essential: Determine TnSeq Gene Essentiality

In travis-m-blimkie/TbTnseq: TnSeq pipeline functions by TB

Description

Determine essential genes based on calls or counts from TnSeq programs Tradis or Transit/Gumbel.

Usage

tbt_essential(tool, input_df, cutoff)

Arguments

tool	Name of the tools used to produce raw calls or counts. Currently supports either "Tradis" or "Gumbel".
input_df	Data frame containing the call or count information for each gene. Expects standard columns produced by Tradis or Transit/Gumbel.
cutoff	Desired cutoff for calling a gene essential.

Details

The cutoff should be set based on the number of replicates, e.g. in the case of three replicates, cutoff can be set to 2, specifying an essential call in at least two of three replicates for a gene to be considered overall essential.

By default, a gene is called essential for a given replicate as follows: For Tradis, the read counts must be 0. For Transit/Gumbel, the gene must have a call of "E". All other values are considered nonessential.

Value

tbt_essential

A data frame of essential genes, and containing an additional column denoting essentiality with "ess".

References

None.

See Also

https://www.github.com/travis-m-blimkie/TbTnseq

Examples

tbt_essential(tool = "Tradis",
  input_df = tradis_results,
  cutoff = 2)

travis-m-blimkie/TbTnseq documentation built on July 22, 2019, 7:39 a.m.