ae: Extract a vector of allelic expression ratios

In maialab/daeqtlr: DAEQTL Mapping

Extract a vector of allelic expression ratios

Description

ae() provides a handy shortcut to extract a vector of allelic expression ratios for a DAE SNP on a set of samples.

ae_hom() and ae_het() also extract a vector of allelic expression ratios but for the corresponding homozygous or heterozygous samples of the candidate SNP, respectively.

Usage

ae(dae_snp, ae, samples = rep(TRUE, ncol(ae) - 1), drop_na = TRUE)

ae_hom(dae_snp, candidate_snp, zygosity, ae, drop_na = TRUE)

ae_het(dae_snp, candidate_snp, zygosity, ae, drop_na = TRUE)

Arguments

dae_snp	A string indicating the identifier of the DAE SNP.
ae	A data frame of expression values. Each row is for a locus. The locus identity is indicated in the first column. Remaining columns are samples.
samples	Either a logical or an integer vector indicating which samples in the ae data table are to be selected.
drop_na	Whether to drop NA values in the returned value.
candidate_snp	A string indicating the identifier of the candidate SNP.
zygosity	A data frame of zygosity levels: "hom" for homozygous or "het" for heterozygous. Each row is for a locus. The locus identity is indicated in the first column and named snp. Remaining columns are samples.

Value

A numeric vector of allelic ratios.

Examples

# Let us load some dummy data
zygosity <- read_snp_zygosity(file = daeqtlr_example("zygosity.csv"))
ae <- read_ae_ratios(file = daeqtlr_example("ae.csv"))

# Select all allelic expression ratios of rsX019
ae('rsX019', ae = ae, drop_na = FALSE)

# Select only the first 5 samples
ae('rsX019', ae = ae, samples = 1:10, drop_na = FALSE)
ae('rsX019', ae = ae, samples = 1:10, drop_na = TRUE)

# Use a logical vector to select samples that meet a requirement, e.g.
# heterozygous samples only. Note that `is_het()` is useful here.
(het_samples_for_rsX019 <- is_het(zygosity = zygosity, snp = 'rsX019'))
ae('rsX019', ae = ae, samples = het_samples_for_rsX019, drop_na = FALSE)

# If you want the allelic ratios for samples that are simultaneously:
# - heterozygous for rsX019
# - homozygous for rsX002
(hom_samples_for_rsX002 <- is_hom(zygosity = zygosity, snp = 'rsX002'))
ae(
  dae_snp = 'rsX019',
  ae = ae,
  samples = het_samples_for_rsX019 & hom_samples_for_rsX002,
  drop_na = FALSE
  )

# Or more simply:
ae_hom('rsX019', 'rsX002', zygosity, ae, drop_na = FALSE)

# Compare with the previous
ae_hom('rsX019', 'rsX002', zygosity, ae, drop_na = TRUE)

maialab/daeqtlr documentation built on May 18, 2022, 6:53 a.m.