Description Usage Arguments Details Value
massage a (possibly velocitized) SingleCellExperiment into an infercnv object
1 2 3 4 5 6 7 8 9 10 11 12 |
x |
a SingleCellExperiment |
group_col |
the colData column with cell annotations ("cnv_group") |
ref_prefix |
prefix for reference sample clusters ("normal_") |
obs_prefix |
prefix for tumor sample clusters ("tumor_") |
by_cluster |
add clusters for references and observations? (FALSE) |
downsample |
downsample? (TRUE, |
maxcells |
how many cells per sample per cluster to grab? (100) |
run |
perform infercnv run with "sensible" defaults? (TRUE) |
cutoff |
expression cutoff for infercnv::run (default: guess) |
... |
other arguments for infercnv::run, e.g. |
We do not require or import infercnv, because the requirement for JAGS can
be a showstopper for HPC installations. This function will stop() if the
infercnv package namespace cannot be attached, however, for obvious reasons.
I have no idea why the infercnv
function name was not taken by infercnv
,
but since it wasn't, I stole it. If NumGenesExpressed
is among the colData
columns for the SingleCellExperiment, and run
==TRUE, then this function
will use the former to guess a sensible value for the latter. The velocessor
package also registers a halfway decent show
method for infercnv objects.
1 | an infercnv object
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