load_locus_attrs: Load table of locus attributes

In ShawHahnLab/chiimp: Computational, High-throughput Individual Identification through Microsatellite Profiling

Load table of locus attributes

Description

Load a comma-separated table of locus attributes to use for analysis. This is called automatically during full_analysis, with the data frame then used by analyze_seqs within analyze_dataset.

Usage

load_locus_attrs(fp_locus_attrs, ...)

Arguments

fp_locus_attrs	path to text file.
...	additional arguments passed to load_csv.

Details

Columns Required:

• Locus: Unique identifier for a given locus

• LengthMin: Minimum known allele sequence length for this locus

• LengthMax: Minimum known allele sequence length for this locus

• LengthBuffer: Additional sequence length below LengthMin and above LengthMax to accept for a candidate allele

• Primer: The forward PCR primer sequence for a given locus, used when matching sequences to loci

• ReversePrimer: The reverse PCR primer sequence

Value

data frame of locus attributes

Examples

filename <- system.file("example_locus_attrs.csv", package = "chiimp")
locus_attrs <- load_locus_attrs(filename)

ShawHahnLab/chiimp documentation built on Aug. 20, 2023, 1:41 a.m.