quickPathwayTC: quickPathwayTC

View source: R/quickPathwayTC.R

quickPathwayTCR Documentation

quickPathwayTC

Description

Plots time series data from the pathway of interest. Genes which pass a user defined threshold will be highlighted.

Usage

quickPathwayTC(filt_df, miRNA_exp, mRNA_exp, morethan, threshold,
 pathwayname)

Arguments

filt_df

Dataframe from the matrixFilter function.

miRNA_exp

miRNA data from using the diffExpressRes function on miRNA data.

mRNA_exp

mRNA data from using the diffExpressRes function on miRNA data.

morethan

TRUE or FALSE. Default is TRUE.

threshold

Integer that is user defined. Default is 1.

pathwayname

Character which is the name of pathway of interest. Default is "Pathway".

Value

Line plot of all the genes of interest from a pathway of interest.

Examples

library(org.Mm.eg.db)

miR <- mm_miR[1:100,]

mRNA <- mm_mRNA[1:200,]

MAE <- startObject(miR = miR, mRNA = mRNA)

MAE <- getIdsMir(MAE, assay(MAE, 1), orgDB = org.Mm.eg.db, 'mmu')

MAE <- getIdsMrna(MAE, assay(MAE, 2), "useast", 'mmusculus', orgDB = org.Mm.eg.db)

MAE <- diffExpressRes(MAE, df = assay(MAE, 1), dataType = 'Log2FC',
                     genes_ID = assay(MAE, 3),
                      idColumn = 'GENENAME',
                      name = "miRNA_log2fc")

MAE <- diffExpressRes(MAE, df = assay(MAE, 2), dataType = 'Log2FC',
                     genes_ID = assay(MAE, 7),
                     idColumn = 'GENENAME',
                     name = "mRNA_log2fc")

Filt_df <- data.frame(row.names = c("mmu-miR-145a-3p:Adamts15",
                                   "mmu-miR-146a-5p:Acy1"),
                     corr = c(-0.9191653, 0.7826041),
                     miR = c("mmu-miR-145a-3p", "mmu-miR-146a-5p"),
                     mRNA = c("Adamts15", "Acy1"),
                     miR_Entrez = c(387163, NA),
                     mRNA_Entrez = c(235130, 109652),
                     TargetScan = c(1, 0),
                     miRDB = c(0, 0),
                     Predicted_Interactions = c(1, 0),
                     miRTarBase = c(0, 1),
                     Pred_Fun = c(1, 1))

MAE <- matrixFilter(MAE, miningMatrix = Filt_df, negativeOnly = FALSE,
                   threshold = 1, predictedOnly = FALSE)

quickPathwayTC(filt_df=MAE[[11]], miRNA_exp=MAE[[9]],
               mRNA_exp=MAE[[10]], morethan = TRUE, threshold =1,
               pathwayname = "Test")

Krutik6/TimiRGeN documentation built on Jan. 27, 2024, 7:46 p.m.