tbt_readFiles: Read files from TnSeq output

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

Description

Given a directory containing data files and list of conditions, read the files produced by Tradis or Transit/Gumbel TnSeq pipelines and select the gene name and call or count columns.

Usage

tbt_readFiles(tool, conditions, reps, data_folder)

Arguments

tool	Specify tool that produced the results files, either "Tradis" or "Gumbel".
conditions	Names of the conditions, which must match to file names being read.
reps	Number of replicates, which should be the same as the number of files for a given condition.
data_folder	Folder containing all of the files for each condition and all its replicates. Should NOT end with "/".

Details

Designed as the first step in a pipeline to determine essential genes from Tradis or Transit/Gumbel. After this step, count or call column (depending on the tool) should be renamed to be unique to each condition/replicate. This can be done using TbTnseq::tbt_rename().

Value

tbt_readFiles

A list of the conditions, holding a list of the replicates for that condition, with the data stored in a data frame. I.e. a list of list of data frames.

References

None.

See Also

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

Examples

# Set up required info
conditions <- list("MHB_unt", "MHB_AZM")

reps <- c("rep1", "rep2", "rep3")

tradis_path <- "Data/Tradis"

# Run tbt_readFiles()
tradis_select_dfs <- tbt_readFiles(tool = "Tradis",
                                   conditions = conditions,
                                   reps = reps,
                                   data_folder = tradis_path)

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