Batch run of opening_act2 function

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.

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):

  1. path Path to bedGraph file.

  2. genotype String indicating the relevant strain mutations, used as the namesake argument to opening_act2.

  3. chip_target String indicating the ChIP target protein, to be used as the namesake argument to opening_act2.

  4. 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:

  1. "SK1Yue"

  2. "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/')
# }