Description Usage Arguments Details Value References See Also Examples
View source: R/tbt_essential.R
Determine essential genes based on calls or counts from TnSeq programs Tradis or Transit/Gumbel.
1 | tbt_essential(tool, input_df, cutoff)
|
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. |
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.
tbt_essential |
A data frame of essential genes, and containing an additional column denoting essentiality with "ess". |
None.
https://www.github.com/travis-m-blimkie/TbTnseq
1 2 3 | tbt_essential(tool = "Tradis",
input_df = tradis_results,
cutoff = 2)
|
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