get_refTP: Get reference expression profiles matching sample age...

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

Get reference expression profiles matching sample age estimates.

Description

Fetches the (indices of, or) expression profiles of a reference that correspond to the input age estimates. Matching reference data can be used to quantify the developmental signal between experimental groups where the variable of interest is confounded by development.

Usage

get_refTP(ref, ae_obj = NULL, ae_values = NULL, return.idx = TRUE)

Arguments

ref	a ref object (as returned by make_ref)
ae_obj	an ae object (as returned by ae)
ae_values	age estimate values (used if ae_obj is NULL).
return.idx	if TRUE (default) returns reference indices. If FALSE, returns reference expression matrix

Value

either a vector of indices (if return.idx is True) or an expression matrix for selected reference time points.

Examples

requireNamespace('wormRef', quietly = TRUE)

# get sample gene expression data
X <- wormRef::Cel_larval$g[,1:9]

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

# define groups
fac <- factor(c('a', 'a', 'b', 
                'a', 'b', 'b',
                'c', 'c', 'c'))

# estimate sample age
ae_X <- ae(X, ref)

# compare group diff. expr. with matching reference
rc <- ref_compare(X, ref, fac, ae_X)
print(rc)

# get sample and reference (ie. development) logFCs between groups
lfc_a_vs_b <- get_logFC(rc)
lfc_a_vs_c <- get_logFC(rc, l = 'c')
lfc_b_vs_c <- get_logFC(rc, l0='b', l = 'c')

# plot sample vs. reference logFCs
par(mfrow = c(2,2))
plot(ae_X, groups = fac)
plot(lfc_a_vs_b, main = 'a vs. b logFC')
plot(lfc_a_vs_c, main = 'a vs. c logFC')
plot(lfc_b_vs_c, main = 'b vs. c logFC')

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