sc3_calc_biology: Calculate DE genes, marker genes and cell outliers.

Description Usage Arguments Details Value

Description

This function calculates differentially expressed (DE) genes, marker genes and cell outliers based on the consensus SC3 clusterings.

Usage

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sc3_calc_biology.SingleCellExperiment(object, ks, regime)

## S4 method for signature 'SingleCellExperiment'
sc3_calc_biology(object, ks = NULL,
  regime = NULL)

Arguments

object

an object of SingleCellExperiment class

ks

a continuous range of integers - the number of clusters k to be used for SC3 clustering. Can also be a single integer.

regime

defines what biological analysis to perform. "marker" for marker genes, "de" for differentiall expressed genes and "outl" for outlier cells

Details

DE genes are calculated using get_de_genes. Results of the DE analysis are saved as new columns in the featureData slot of the input object. The column names correspond to the adjusted p-values of the genes and have the following format: sc3_k_de_padj, where k is the number of clusters.

Marker genes are calculated using get_marker_genes. Results of the marker gene analysis are saved as three new columns (for each k) to the featureData slot of the input object. The column names correspond to the SC3 cluster labels, to the adjusted p-values of the genes and to the area under the ROC curve and have the following format: sc3_k_markers_clusts, sc3_k_markers_padj and sc3_k_markers_auroc, where k is the number of clusters.

Outlier cells are calculated using get_outl_cells. Results of the cell outlier analysis are saved as new columns in the phenoData slot of the input object. The column names correspond to the log2(outlier_score) and have the following format: sc3_k_log2_outlier_score, where k is the number of clusters.

Additionally, biology item is added to the sc3 slot and is set to TRUE indicating that the biological analysis of the dataset has been performed.

Value

an object of SingleCellExperiment class


SC3 documentation built on May 2, 2018, 2:08 a.m.