plot_primiRNA: Plot the result of prediction for miRNA
In primirTSS: Prediction of pri-miRNA Transcription Start Site

Description Usage Arguments Details Value Examples

View source: R/plot_miRNA_track.R

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.

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
)

`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.

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

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.

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)