heatMapRegion {ORFik} | R Documentation |
Simplified input space for easier abstraction of coverage heatmaps
Pick your region and plot
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, format = ".png", acceptedLengths = 21:75, upstream = c(50, 30), downstream = c(29, 69), shifting = c("5prime", "3prime") )
df |
an ORFik |
region |
a character, default "TIS", can be any combination of the set: c("TSS", "TIS", "TTS"), which are: Transcription start site (5' end of mrna), Translation initation site (5' end of CDS), Translation termination site (3' end of CDS) |
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 |
format |
a character, default ".png", alternative ".pdf" |
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) |
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")