Post-inForm

Post-process cell immunofluorescence data produced by the inForm software.

Dependencies

The following R libraries are needed to run Post-inForm:

• openxlsx
• zip
• checkmate

These can be installed with the following R command: install.packages(c("openxlsx", "zip", "checkmate"))

Examples of how to run Post-inForm

Load Post-inForm source code:

Download or clone the project's directory to your local machine. Then set POSTINFORM_ROOT to the postinform directory on your local machine and run the source() command in your R console, as shown here:

POSTINFORM_ROOT = '~/projects/chuv_cte/postinform.git'
source(file.path(POSTINFORM_ROOT, 'R', 'config.R'), chdir=TRUE)

Process samples:

Post-inForm can be run with 3 different commands:

• check: check input data only. Does not produce any output.
• reduce: reduce size of input data by deleting all unecessary data from input. For standard inForm data, the reduction in size is approximatively of a factor 10.
• process: run the full Post-inForm data processing pipeline.

input_file = 'Session_Batch6_1_Curry2.zip'
postinform(input_file_or_dir=input_file, command='check')
postinform(input_file_or_dir=input_file, command='reduce')
postinform(input_file_or_dir=input_file, command='process')

Post-inForm options:

• compress_output: if TRUE, the output is compressed to a .zip file. If FALSE the output remains in an uncompressed directory.
• allow_overwrite: if TRUE, pre-existing files and directories with the same name as an output file or directory are silently and mercylessly deleted. Leave this to FALSE to avoid accidental deletions.
• output_suffix: suffix to be appended to the input file or directory name to form the output name. E.g. if the input file is named Test_session.zip and output_suffix is set to processed, then the ouput will be named Test_session_processed. By default, the suffix value is set to reduced when running the "reduce" command, and processed when running the "process" command.
• immucan_output: if TRUE, produces IMMUCAN compatible outputs.

Examples:
This command will produce an uncompressed output directory "Test_session_reduced". If such a directory already exists, it will be overwritten since "allow_overwrite" is set to TRUE

postinform(input_file_or_dir="Test_session.zip", command='reduce',
         compress_output=F, immucan_output=FALSE, allow_overwrite=TRUE)

This command will produce an output file named "Test_session_random_suffix.zip".

postinform(input_file_or_dir="Test_session.zip", command='process', output_suffix="random_suffix",
         compress_output=TRUE, immucan_output=TRUE, allow_overwrite=FALSE)

Post-inForm input parameter file format.

The list of samples, tissues, markers and marker combinations to process are passed to post-inForm via a single plain text file that must be named parameters.txt and be located at the root of the input directory. Important: for Windows users, the parameters.txt file should be encoded in UTF-8

The parameters input file must contain the following 5 sections. For each section, values can be passed on the same line separated by a ,, or on multiple lines (one value per line). Any line starting the a # value is ignored (allows to add comments to file).
For the marker_combinations: section, the special value all can be passed to process all possible combinations of markers (to avoid having to enter all combinations manually).

samples:
tissues:
phenotyped_markers:
scored_markers: 
marker_combinations: 

A template file can be downloaded here.
parameters.txt file example:

# List of samples to process.
samples:
SAMPLE_1
SAMPLE_2
SAMPLE_3

# List of tissues to process.
tissues: stroma, tumor

# List of markers.
phenotyped_markers: CD20, CD3, CD68
scored_markers: 

# Marker combinations to test
marker_combinations: all