Topic_func_anno: Annotating each topic's function.

In BinDuan/MASCOT: Model-based Analysis of Single cell CRISPR knockOuT screening

Description

After calculating topics, MASCOT obtains the occurring probabilities of genes available in each topic. For each topic, genes with large probabilities were used to annotate the topic<e2><80><99>s function. Specifically, MASCOT firstly selects the n% top-ranked (default 20%) genes of each topic based on their occurring probabilities. Then these genes were used to perform the functional enrichment annotation with R package clusterProfiler together with a FDR correction. Finally the top-ranked n (default 5) GO terms were selected to represent each topic<e2><80><99>s key functions.

Usage

Topic_func_anno(model, species = "Hs", topGene_percent = 0.2, topNum = 5, FDR = 0.1, plot = TRUE, plot_path = "~/topic_annotation.pdf")

Arguments

model	Object of class "LDA" with the optimal topic number.
species	The species the cells belong to. Currently species="Hs" for homo sapiens or species="Mm" for mus musculus are available.
topGene_percent	The top percentage of genes selected to annotate the topic's function(default 20%).
topNum	The top-ranked number (default 5) GO terms were selected to represent each topic<e2><80><99>s key functions.
FDR	False discovery rate(default 0.1).
plot	TRUE by default. If FALSE, don't plot the graph.
plot_path	The path of the graph you plot. It works only when the parameter "plot" is TRUE.

Value

A dataframe showing the annotation result.

Author(s)

Bin Duan

References

Yu G, Wang LG, Han Y, He Q. Y. clusterProfiler: an R package for comparing biological themes among gene clusters. Omics. 2012;16:284<e2><80><93>287. doi: 10.1089/omi.2011.0118.

BinDuan/MASCOT documentation built on May 23, 2019, 2:42 p.m.