Description
Usage
Arguments
Value
References
View source: R/findIndex.R
Find a reasonable set of genes (one mode and at least 25
to use for simulation.
SCdat |
An object of class SingleCellExperiment that contains
normalized single-cell expression and metadata. The assays
slot contains a named list of matrices, where the normalized counts are
housed in the one named normcounts. This matrix should have one
row for each gene and one sample for each column.
The colData slot should contain a data.frame with one row per
sample and columns that contain metadata for each sample. This data.frame
should contain a variable that represents biological condition, which is
in the form of numeric values (either 1 or 2) that indicates which
condition each sample belongs to (in the same order as the columns of
normcounts). Optional additional metadata about each cell can also
be contained in this data.frame, and additional information about the
experiment can be contained in the metadata slot as a list.
|
condition |
A character object that contains the name of the column in
colData that represents
the biological group or condition of interest (e.g. treatment versus
control). Note that this variable should only contain two
possible values since scDD can currently only handle two-group
comparisons. The default option assumes that there
is a column named "condition" that contains this variable.
|
Vector of indices for a reasonable set of genes that can be used
for simulation.
Korthauer KD, Chu LF, Newton MA, Li Y, Thomson J, Stewart R,
Kendziorski C. A statistical approach for identifying differential
distributions
in single-cell RNA-seq experiments. Genome Biology. 2016 Oct 25;17(1):222.
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1077-y
scDD documentation built on Nov. 8, 2020, 7:10 p.m.
