importing_data: Parse common allele frequency data formats

Description Usage Arguments Details Value

Description

Reads a tabular data file and generates a freqt object. Supports multiple common data sources:

Usage

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read_popstr(filename, name = "")

read_nist(filename, name = "")

read_familias(filename, name = "")

read_strider(filename, name = "", origin = "")

Arguments

filename

the path to the relevant CSV file

name

the name to give to the dataset

origin

(only for read_strider) which population group to choose

Details

read_popstr

supports reading from CSV files downloaded from the pop.STR project website. No modification of the files is required.

read_nist

Supports reading from CSV files generated from NIST STRBase data. NIST data comes in MS Excel files with multiple sheets and additional formating. This function expexts a CSV file with only one of those sheets.

read_familias

Supports reading from a Familias frequency database file. The Familias importer does not support reading the number of individuals as it is not included in Familias data files.

read_strider

Supports extracting frequency data from the STRidER 2.0 XML database. Requires that the parameter origin is supplied and that it matches one of the keys in the STRidER database.

Value

a freqt object with the given data


knifecake/fafreqs documentation built on March 13, 2020, 11:53 p.m.