summarize.batches {RPA} | R Documentation |
Summarize batches.
summarize.batches(sets = NULL, probe.parameters = list(), batches, load.batches = FALSE, mc.cores = 1, cdf = NULL, bg.method = "rma", normalization.method = "quantiles", verbose = TRUE, save.batches.dir = ".", unique.run.identifier = NULL, save.batches = FALSE, set.inds, speedup = FALSE, summarize.with.affinities = FALSE)
sets |
Probesets to summarize |
probe.parameters |
Optional probe parameters, including priors. |
batches |
Data batches for online learning |
load.batches |
Logical. Load precalculated data for the batches. |
mc.cores |
Number of cores for parallel computation |
cdf |
CDF for alternative probeset definitions |
bg.method |
Background correction method |
normalization.method |
Normalization method |
verbose |
Print progress information |
save.batches.dir |
Specify the output directory for temporary batch saves. |
unique.run.identifier |
Define identifier for this run for naming the temporary batch files. By default, a random id is generated. |
save.batches |
Save batches? |
set.inds |
Probeset indices |
speedup |
Speed up calculations with approximations. |
summarize.with.affinities |
Use affinity estimates in probe summarization step. Default: FALSE. |
Sweeps through the batches. Summarizes the probesets within each batch based on the precalculated model parameter point estimates.
Expression matrix: probesets x samples.
Leo Lahti leo.lahti@iki.fi
See citation("RPA")
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