load_config: Load and validate configuration file

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

Description

WGSAParsr configuration files are flexible tab-separated files. They must include a header with field names, and the following fields, in any order:

• field column headings matching the WGSA output file to be parsed

• SNV logical (TRUE/FALSE) indicating whether the field should be parsed for snv annotation

• indel logical (TRUE/FALSE) indicating whether the field should be parsed for indel annotation

• dbnsfp logical (TRUE/FALSE) indicating whether the field should be parsed for dbnsfp annotation

• pivotGroup numerical value to group annotations for pivoting

• pivotChar character separating fields that should be used for pivoting

• parseGroup numerical value to group annotations for other parsing

• transformation a string describing the transformation to be performed. Values may include:

  • max select the maximum value

  • min select the minimum value

  • pick_Y select "Y" if present

  • pick_N select "N" if present

  • pick_A select A>D>P>N (MutationTaster_pred field)

  • clean remove the {n}. E.g.: "Enhancer{4}" -> "Enhancer"

  • distinct select unique values. NOTE: must have a pivotGroup and pivotChar = |

Usage

load_config(config_path)

Arguments

config_path

Path to the WGSAParsr configuration file to load and validate

Details

Additionally, the following fields may be included, and are processed during configuration file loading, but are not required:

• outputOrder numerical value for column ordering in parsed output #'

• outputName a string that should be used for the field name in the output file (useful for renaming fields)

• toRemove any characters to remove in the output tsv. For example, if a WGSA field uses a character used to encode a NULL value, it may need to be removed to facilitate database import. If this field is included in the config file, WGSAParsr will convert the specified string to a blank field in output

• pivotChar2 character separating fields that should be used for a second level of pivoting (as required for newer dbnsfp field format - e.g. foo;bar|waa;woo may need to be pivoted on the '|' and the ';' characters)

Other columns (such as notes) may be included in the configuration file, but will not be validated or imported with this function. The configuration file may include comments beginning with #.

Value

a tibble that can be used for building field lists for parsing

Examples

## Not run: 
local_config <- load_config("config.tsv")

## End(Not run)

freeze_5_config <- load_config(wgsaparsr_example("fr_5_config.tsv"))

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