plot_primiRNA {primirTSS} | R Documentation

## Plot the result of prediction for miRNA

### Description

For each miRNA, plot the position of TSS, pri-miRNA, related Ensemble gene, eponine socre and conservation score according to the result of prediction using primirTSS.

### Usage

    plot_primiRNA(expressed_mir, bed_merged, flanking_num = 1000,
      threshold = 0.7, ignore_DHS_check = TRUE, DHS,
      allmirdhs_byforce = TRUE, expressed_gene = "all",
      allmirgene_byforce = TRUE)

### Arguments

`expressed_mir` | This parameter allows users to specify certain miRNAs, the TSSs of which they want to search for by providing a list of miRNAs(e.g. expressed miRNAs in a certain cell-line). If `expressed_mir` is not specified, the default value of the parameter is "`all`" and the function will acquiescently employ all the miRNAs currently listed on "`miRbase`" database.
`bed_merged` | Peaks from ChIP-seq data to be provided for analysis can be H3K4me3 peaks, Pol II peaks or both. Notice that peaks are supposed to be merged(see also `peak_merge`) before `find_TSS` if using only one kind of peak data, while peaks shoud be firstly merged and then join together(see also `peak_join`) if both H3K4me3 data and Pol II are input.
`flanking_num` | A parameter in Eponine model to detect TSSs. It is concluded that a peak signal with flanking regions of C-G enrichment are important to mark TSSs. The default value is 1000.
`threshold` | Threshold for candidate TSSs scored with Eponine method. The default value is 0.7.
`ignore_DHS_check` | The process of DHS_check further assist to filter putative TSSs. When there are a DHS peak that locates within 1 kb upstream of a putative TSS, this predicted TSS will be retain for it character is consistent with that of an authentic TSS. Or the TSSs with no DHSs locating within 1 kb upstream of them would be discard.
`DHS` | ChIP-seq data of DNase I hypersensitive sites(DHSs).
`allmirdhs_byforce` | When we use DHS data to check the validity of TSSs, there is possibility where no DHSs locates within 1 kb upstream of all putative TSSs and all these putative TSSs might be filtered out by our method resulting no outputs. While "`allmirdhs_byforce` = TRUE", it ensures to output at least 1 most possible TSS even if the nearest DHS signal locates more than 1 kb upsteam of this TSS.
`expressed_gene` | Users can speicify genes expressed in certain cell-lines that is analyzed. Or the default value is "`all`", which means all the expressed genes annotated on Ensemble will be employed.
`allmirgene_byforce` | While integrating expressed_gene data to improve prediction, there might be a circumstance where all the putative TSS are discarded. To prevent this condition, users are allowed to use "`allmirgene_byforce = TRUE`" to ensure at least 1 putative TSS for each miRNA will be output.

### Details

NOTICE that this function is used for visualizing the predicted result of ONLY ONE specific miRNA every single time.

### Value

There will be six tracks plotted as return:

`Chrom`: Position of miRNA on the chromosome.

`hg38`: Reference genome coordinate in hg38.

`pri-miRNA`: Position of pri-miRNA.

`Ensemble genes`: Position of related protein-coding gene.

`eponine score`: Score of best putative TSS conducted by eponine method.

`conservation score`: Conservation score should be integrated with eponine score to find out putative TSSs.

### Examples

    expressed_mir <- "hsa-mir-5697"
    bed_merged <- data.frame(
      chrom = c("chr1", "chr1", "chr1", "chr1", "chr2"),
      start = c(9180799, 9201483, 9234339, 9942202, 9830615),
      end = c(9183889, 9202580, 9235853, 9944469, 9917994),
      stringsAsFactors = FALSE
    )
    bed_merged <- as(bed_merged, "GRanges")
    ## Not run:
    plot_primiRNA(expressed_mir, bed_merged)

    ## End(Not run)

[Package primirTSS version 1.4.0 Index]