BASiCS_ParallelMCMC: Parallelized BASiCS_MCMC
In oliviermfmartin/HelpingHand: A helping hand

Description Usage Arguments Details Value See Also

Parallelize BASiCS normalization implemented in BASiCS_MCMC.

BASiCS_ParallelMCMC(
  CountsList,
  SpikeInfo,
  N = 200000L,
  Burn = 80000L,
  Thin = 40L,
  Regression = TRUE,
  MinCount = 10L,
  PropMinCount = 0.85,
  NCores = 2L,
  Name = paste0(sample(c(0:9, letters), 10), collapse = ""),
  Verbose = TRUE
)

`CountsList`	A list of unfiltered count matrices with genes as rows and samples as columns.
`SpikeInfo`	`data.frame` whose first and second columns contain the gene names assigned to the spike-in genes (they must match the ones in `rownames(Counts)`) and the associated input number of molecules, respectively. If `SpikeInfo = NULL`, only the horizontal integration implementation (no spikes) can be run. Default value: `SpikeInfo = NULL`.
`N`	Total number of iterations for the MCMC sampler. Use `N>=max(4,Thin)`, `N` being a multiple of `Thin`.
`Burn`	Burn-in period for the MCMC sampler. Use `Burn>=1`, `Burn<N`, `Burn` being a multiple of `Thin`.
`Thin`	Thining period for the MCMC sampler. Use `Thin>=2`.
`Regression`	If `Regression = TRUE`, BASiCS exploits a joint prior formulation for mean and over-dispersion parameters to estimate a measure of residual over-dispersion is not confounded by mean expression. Recommended setting is `Regression = TRUE`.
`MinCount`	integer; Minimum number of counts for a gene.
`Name`	character; Chain identification name.
`PropMinCount;`	numeric; Proportion of samples with minimum count.
`NCores;`	integer; Number of cores.
`Verbose;`	bool; Print progress in `./logs` directory?

Assumes that there are spike-ins and that these are named "ERCC". Filter rule: a gene must be counted at least MinCount in PropMinCount percent of the samples. For biological transcripts, this needs to be true in at least one group. For spike-ins in all the groups. Uses mclapply to parallelize.

A list of BASiCS_Chain object.

BASiCS_Chain

BASiCS_MCMC

oliviermfmartin/HelpingHand documentation built on Oct. 10, 2020, 5:59 a.m.