et_essential: et_essential

In hancockinformatics/EssentialTnSeq: TnSeq Essentiality Analysis

Description

Determines essentiality for a set of genes from Gumbel or Tradis. For Gumbel, a gene is considered essential if it was assigned a call of "E". For Tradis, essential genes are those with 0 read counts. The filtered data frame which is returned contains the additional columns used in defining essentiality.

Usage

et_essential(tool, input_df, cutoff, filter = TRUE)

Arguments

tool	String; one of "Gumbel" or "Tradis".
input_df	Data frame containing essentiality call for all replicates for a given condition.
cutoff	Threshold for determining essentiality based on the number of replicates. Recommend setting to one less than the number of replicates.
filter	If TRUE (default), the result returned to the user is filtered to only contains the genes determined essential. If FALSE, the unfiltered data frame is returned instead.

Value

Filtered data frame of essential genes for the condition.

References

None.

See Also

https://github.com/hancockinformatics/EssentialTnSeq

Examples

## Not run: 
  et_essential("Gumbel", treatment1_df, cutoff = 2, filter = TRUE)

## End(Not run)

hancockinformatics/EssentialTnSeq documentation built on July 23, 2020, 9:56 a.m.