opening_act2_batch_run: Batch run of 'opening_act2' function

In hochwagenlab/hwglabr2: Collection of R functions used in the Hochwagen Lab

Batch run of opening_act2 function

Description

This function will take a CSV file containing the path to multiple data folders and argument labels and run opening_act2 function for each data set in the file. It allows you to run a batch of data sets automatically.

Usage

opening_act2_batch_run(
  input_data_file,
  ref_genome,
  output_path = "/Volumes/LabShare/HTGenomics/Opening_act/"
)

Arguments

input_data_file	String indicating path to file containing instructions. The file must be in CSV format with the following columns (column names in the file must be reproduced exactly as below): path Path to bedGraph file. genotype String indicating the relevant strain mutations, used as the namesake argument to opening_act2. chip_target String indicating the ChIP target protein, to be used as the namesake argument to opening_act2. sample_id The sample ID, to be used as the namesake argument to opening_act2. No default.
ref_genome	Character object specifying the genome version, to be used as the genome argument to opening_act2; accepts one of the following options: "SK1Yue" "sacCer3" No default.
output_path	Character object with a valid path to directory to save output files at. Defaults to '/Volumes/LabShare/HTGenomics/Opening_act/'.

Examples

## Not run: 
opening_act_batch_run(input_data_file="~/Desktop/inputs.csv",
                      ref_genome="SK1Yue")

opening_act_batch_run(input_data_file="~/Desktop/inputs.csv",
                      ref_genome="sacCer3", output_path='~/Desktop/')

## End(Not run)

hochwagenlab/hwglabr2 documentation built on Nov. 12, 2022, 7:27 p.m.