check_project: Check consistency of data in a project

In jiho/zooprocessr: Read and analyse data generated by zooprocess

Description

Check consistency of data in a project

Usage

check_project(project)

## S3 method for class 'checklist'
print(x, nmax = 50)

Arguments

project	path to the project directory
nmax	maximum number of problematic items to print out (50 by default)

Details

This function

1. Reads the metadata table of the project

2. Lists and reads all dat1.pid files in the work directory

3. Lists and reads all dat1.tx files in PID_process/Pid_results/Dat1_validated (or Dat1_extracted if the previous one is empty)

4. Lists all images in the PID_process/Sorted_vignettes directory

Then it

1. Compares the list of samples in the metadata, dat1.pid, and dat1.txt files

2. Compares the list of objects in the dat1.pid, dat1.txt files, and present as images (i.e. vignettes)

3. For images present both in the dat1.txt files and as vignettes, checks that the location of a vignette (its classification) matches the last column in the dat1.txt file

Value

Returns a list (of class check) containing all problematic items (sample or object names) that can be printed with various levels of detail (depending on nmax)

jiho/zooprocessr documentation built on May 19, 2019, 10:31 a.m.