fit_cds_vglm: Fit vector generalized linear model to a CellDataSet object

In jacobheng/cellwrangler: Supplemental toolkit for single-cell RNAseq analysis

Description

fit_cds_vglm() is a wrapper function around the monocle::fitModel() function that fits a vglm for each gene in a CellDataSet object and return a dataframe with the estimate, standard error, z value and p-value for each coefficient specified in the model formula string.

Usage

fit_cds_vglm(cds, modelFormulaStr, test_cds = NULL,
  test_genes = c("Actb"), monocle3 = F)

Arguments

cds	a monocle CellDataSet object
modelFormulaStr	model formula string specifying the model to fit for the genes
test_cds	a monocle CellDataSet object to be used for error trapping; if NULL, cds will be used as test_cds.
test_genes	genes to test the model on, for error trapping; test_genes must be expressed in test_cds object.

Examples

find_cds_vglm(dat)

jacobheng/cellwrangler documentation built on Aug. 12, 2019, 6:49 a.m.