validate_config: Validate configuration tibble

In UW-GAC/wgsaparsr: A R package for Parsing Annotation File for Database Import

Description

WGSAParsr configuration can be loaded from a file with load_config() or passed as a data frame/tibble. This function validates the tibble as meeting the following criteria:

Usage

validate_config(config_tibble)

Arguments

config_tibble

tibble containing parsing configuration details.

Details

Contains required columns: "field", "SNV", "indel", "dbnsfp", "pivotGroup", "pivotChar", "parseGroup", "transformation".

the SNV, indel, and dbnsfp fields may contain NA or logical values

the transformation field may contain NA or "max", "min", "pick_Y", "pick_N", "pick_A", "clean", "distinct".

all members of each pivotGroup must have the same pivotChar (and pivotChar 2, if defined)

fields that have a pivotChar value must have a pivotGroup value

fields that have a pivotChar2 value must have a pivotChar

a parseGroup may not have multiple transformations

Examples

## Not run: 

validate_config(config_tibble)

## End(Not run)

UW-GAC/wgsaparsr documentation built on Aug. 9, 2020, 5:50 a.m.