methodWrapper.scde: SCDE

In jhsiao999/ashbun: Methods and evaluation tools for single cell RNA-seq count data

Description

Implement SCDE 1.99.2. This older version of SCDE is need for computers that are compatible with an older version of flexmix (flexmix_2.3-13; for related discussions on this, see https://github.com/hms-dbmi/scde/issues/40). Currently, this function uses the SCDE method for normalizatino and does not allow using other normalization factors.

Usage

methodWrapper.scde(counts, condition, control = list(save_modelFit = FALSE,
  n.randomizations = 100, n.cores = 4, min.size.entries = ncol(counts)))

Arguments

counts	Gene by sample expression count matrix (G by N).
condition	Binary vector of length N indicating sample biological condition.
control	List with control arguments, including save_modelFit TRUE to output the complete DESeq2 fit results. n.randomization SCDE internal argument: Nubmer of bootstraps. n.cores SCDE internal argument: Nubmer of cores. min.size.entries SCDE internal argument: Mininum number of genes to use when determining expected expression magnitude during model fitting.

Value

List with the following objects sig_order Z-socres of expression difference, ordered from the most significant to the least significant. fit SCDE complete output of the model fit.

Author(s)

Chiaowen Joyce Hsiao

jhsiao999/ashbun documentation built on May 8, 2019, 11:17 p.m.