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Convert a NACHO 2 object to NACHO 3

Source: R/read_nacho.R
upgrade_nacho.Rd

NACHO 3 stores data in an S7 nacho object instead of the NACHO 2 list. upgrade_nacho() converts a NACHO 2 object once: it keeps the raw counts, the sample sheet, the settings and the thresholds, and computes the quality-control metrics, the normalised counts, the PCA and the outlier flags again with the NACHO 3 definitions.

Usage

upgrade_nacho(x)

Arguments

x

A NACHO 2 object, as returned by load_rcc() or normalise() in NACHO 2.

Value

A nacho object.

See also

read_nacho()

Examples

# A NACHO 2 object is converted; GSE74821 is already a NACHO 3 object,
# so it comes back unchanged.
data(GSE74821)
identical(upgrade_nacho(GSE74821), GSE74821)
#> `x` is already a NACHO 3 object, so it is returned unchanged.
#> [1] TRUE