ae: Age Estimate

In LBMC/wormAge: Real Age Prediction from Transcriptome staging On Reference

Age Estimate

Description

ae estimates the developmental age of input samples based on correlation with the given reference data.

Usage

ae(
  samp,
  refdata,
  ref.time_series = NULL,
  cor.method = "spearman",
  nb.cores = 2,
  bootstrap.n = 30,
  bootstrap.set_size = NULL,
  prior = NULL,
  prior.params = NULL,
  verbose = T
)

Arguments

samp	sample matrix, genes as rows, individuals as columns
refdata	a reference object, as returned by make_ref, or a reference time series matrix in same format as samp
ref.time_series	ignored if a ref object is given to refdata, else the time values of the reference data specified)
cor.method	correlation method, one of "spearman" (default) or "pearson".
nb.cores	number of cores for parallelism, defaults to 2.
bootstrap.n	number of bootstraps. Defaults to 30, should be >5.
bootstrap.set_size	random gene set size for the bootstrap, defaults to n/3 (with n, the size of the sample-reference gene set overlap).
prior	Approximate time values for each sample, in the time unit of the given reference. Values are recycled if less than the number of samples
prior.params	Standard deviation of the prior scoring distribution. Setting this value too low can cause a significant bias in the age estimation.
verbose	if TRUE (default), displays progression messages.

Details

Confidence intervals for each estimate are computed from bootstrapping on genes and computing the Median Absolute Deviation of the bootstrap age estimates to the global estimate.

A prior can be given to help with the estimate, in which case the peaks of the correlation profiles will be scored according to a gaussian of the specified parameters.

Value

an ae object, with the age estimates, the correlation matrix between sample and reference, the reference time series, and the bootstrap age estimates and correlation matrices. There are plot, print and summary methods for this object.

Examples

requireNamespace('wormRef', quietly = TRUE)

# get some samples to stage
samp <- wormRef::Cel_larval$g[,13:15]

# load interpolated reference
r_larv <- prepare_refdata(ref = 'Cel_larval', datapkg = 'wormRef' , n.inter = 200)

# perform age estimate
ae_test <- ae(samp, r_larv)

# check output
summary(ae_test)
plot(ae_test) # plot all sample estimates
plot_cor(ae_test) # plot individual correlation profiles of samples

# get results
ae_test$age.estimates

LBMC/wormAge documentation built on April 6, 2023, 3:52 a.m.