similarity_score | R Documentation |

Compute the similarity between a predefined condition grouping and the sample cluster of each module, which is defined as the Adjusted Rand index between the two vectors, or the inverse of K-L divergence between the upper triangle matrix of the pairwise distance of predefined ranked condition grouping and the pairwise distance of sample cluster of each module.

similarity_score(gnet_result, group, ranked = FALSE)

`gnet_result` |
Returned results from gnet(). |

`group` |
predefined condition grouping |

`ranked` |
the grouping information is categorical(treatment/control) or ordinal(dosage, time points)? |

A list of similarity scores between a predefined condition grouping and the sample cluster of each module, and the p values for the similarity scores based on permutation.

set.seed(1) init_group_num = 8 init_method = 'kmeans' exp_data <- matrix(rnorm(50*10),50,10) reg_names <- paste0('TF',1:5) rownames(exp_data) <- c(reg_names,paste0('gene',1:(nrow(exp_data)-length(reg_names)))) colnames(exp_data) <- paste0('condition_',1:ncol(exp_data)) se <- SummarizedExperiment::SummarizedExperiment(assays=list(counts=exp_data)) gnet_result <- gnet(se,reg_names,init_method,init_group_num) s <- similarity_score(gnet_result,rep(1:5,each = 2))

chrischen1/GNET2 documentation built on June 29, 2022, 8:53 a.m.

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