heatMapRegion {ORFik} | R Documentation |
Simplified input space for easier abstraction of coverage heatmaps
Pick your transcript region and plot directly
Input CAGE file if you use TSS and want improved 5' annotation.
heatMapRegion( df, region = "TIS", outdir = "default", scores = c("transcriptNormalized", "sum"), type = "ofst", cage = NULL, plot.ext = ".pdf", acceptedLengths = 21:75, upstream = c(50, 30), downstream = c(29, 69), shifting = c("5prime", "3prime"), longestPerGene = FALSE )
df |
an ORFik |
region |
a character, default "TIS", can be any combination of the set: c("TSS", "TIS", "TTS", "TES"), which are: Transcription start site (5' end of mrna), Translation initation site (5' end of CDS), Translation termination site (3' end of CDS), Transcription end site (3' end of 3' UTRs) |
outdir |
a character path, default: "default", saves to:
|
scores |
character vector, default c("transcriptNormalized", "sum"), either of zscore, transcriptNormalized, sum, mean, median, .. see ?coverageScorings for info and more alternatives. |
type |
character, default: "ofst". Type of library: either "default", usually bam format (the one you gave to experiment), "pshifted" pshifted reads, "ofst", "bed", "bedo" optimized bed, or "wig" |
cage |
a character path to library file or a |
plot.ext |
a character, default ".pdf", alternative ".png" |
acceptedLengths |
an integer vector (NULL), the read lengths accepted. Default NULL, means all lengths accepted. |
upstream |
1 or 2 integers, default c(50, 30), how long upstream from 0 should window extend (first index is 5' end extension, second is 3' end extension). If only 1 shifting, only 1 value should be given, if two are given will use first. |
downstream |
1 or 2 integers, default c(29, 69), how long upstream from 0 should window extend (first index is 5' end extension, second is 3' end extension). If only 1 shifting, only 1 value should be given, if two are given will use first. |
shifting |
a character, default c("5prime", "3prime"), can also be either or NULL (no shifting of reads) |
longestPerGene |
logical (TRUE), return only longest valid transcript per gene. NOTE: This is by priority longest cds isoform, if equal then pick longest total transcript. So if transcript is shorter but cds is longer, it will still be the one returned. |
invisible(NULL), plots are saved
Other heatmaps:
coverageHeatMap()
,
heatMapL()
,
heatMap_single()
# Toy example, will not give logical output, but shows how it works df <- ORFik.template.experiment()[3,] # Only third library #heatMapRegion(df, "TIS", outdir = "default") # # Do also TSS, add cage for specific TSS # heatMapRegion(df, c("TSS", "TIS"), cage = "path/to/cage.bed") # Do on pshifted reads instead of original files remove.experiments(df) # Remove loaded experiment first # heatMapRegion(df, "TIS", type = "pshifted")