survival.miR_rna: survival analysis

In leiming8886/fRNC: ncRNA module search functions

survival analysis

Description

The function calculate the P-values from a univariable Cox proportional hazards regression model between survival data and corresponding expression of node. First, the overlap of the sample IDs among the survival data and the two expression data is obtained, then based on the overlap sample IDs, the p-value of every node from a univariable Cox proportional hazards regression model is calculated on the R package survival.

Usage

survival.miR_rna(miRNA_profile = NULL, gene_profile = NULL, clinData = NULL)

Arguments

miRNA_profile	the miRNA expressin data matrix,in which the row name is gene id and the column name is sample id.
gene_profile	the mRNA expressin data matrix,in which the row name is gene id and the column name is sample id.
clinData	the data matrix of survival data,in which the column name is "ID"(sample IDs), "Survival"(months) and "Status"(0,1)

Value

surivallis list contain three elements, miR_p the p-value matrix of IDs, rna_p the p-value matrix of IDs, algorithm a character string indicating which algorithm was used

Examples

## Not run: 
result_miR <- DEGs(case.exp_miRNA,control.exp_miRNA,
geneid= rownames(control.exp_miRNA),data_type = "RNAseq_counts")
result_rna <- DEGs(case.exp_rna,control.exp_rna,
geneid= rownames(control.exp_rna), data_type = "RNAseq_counts")
interac <- interac[,c("node_gene_ID","type","target_gene_ID")]
survival.miR_rna(miRNA_profile=result_miR$Nor_expr,
gene_profile = result_rna$Nor_expr, clinData = clinData)

## End(Not run)

leiming8886/fRNC documentation built on Feb. 21, 2023, 4:12 p.m.