sub-.exstra_tsum: Extract loci or samples from exstra_tsum object

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

Extract loci or samples from exstra_tsum 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_tsum'
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_tsum object

Examples

# Run tsum_test()
(tsum <- tsum_test(exstra_wgs_pcr_2[c("HD", "SCA2", "SCA6", "FRDA")], B = 100))

# All data:
tsum

# Extract one locus:
tsum["HD"]

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

# One sample at one locus:
tsum["HD", "WGSrpt_10"]

# Extract by index 
tsum[2, 5]

# The following are intended to work, but do not at present:
# Extract all triplet repeats
## tsum[unit_length == 3]
## tsum[unit_length == 3]$db$locus

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

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

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