quickPathwayTC {TimiRGeN} | R 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")

[Package TimiRGeN version 1.2.0 Index]