sub-.exstra_score: Extract loci or samples frome exstra_score object

In bahlolab/exSTRa: Expanded STR algorithm: detecting expansions in Illumina sequencing data

Extract loci or samples frome exstra_score object

Description

Using i (select) syntax of data.table to extract loci and/or samples. The first index is the loci filter on x$db, and second sample filter on x$samples.

Usage

## S3 method for class 'exstra_score'
x[loc, samp]

Arguments

x	exstra_score object
loc	Select loci, using data.table filtering on x$db.
samp	Select samples, using data.table filtering on x$samples.

Value

exstra_score object

Examples

# All data:
exstra_wgs_pcr_2

# Extract one locus:
exstra_wgs_pcr_2["HD"]

# Extract one sample:
exstra_wgs_pcr_2[, "WGSrpt_10"]

# Extract all triplet repeats
exstra_wgs_pcr_2[unit_length == 3]
exstra_wgs_pcr_2[unit_length == 3]$db$locus

# Extract all coding repeats
exstra_wgs_pcr_2[gene_region == "coding"]
exstra_wgs_pcr_2[gene_region == "coding"]$db$locus

# Extract all case samples:
exstra_wgs_pcr_2[, group == "case"]

# Extract by index 
exstra_wgs_pcr_2[2, 5]

bahlolab/exSTRa documentation built on Sept. 17, 2022, 5:08 p.m.