fwrite_ucsc: Write USCS genome browser file from intervals set data frame

In tanaylab/misha.ext: A home to functions that extend the misha package

Write USCS genome browser file from intervals set data frame

Description

Write USCS genome browser file from intervals set data frame

Usage

fwrite_ucsc(
  intervals,
  file,
  name,
  type = NULL,
  description = "",
  color = "black",
  rm_intervalID = TRUE,
  append = FALSE,
  span = NULL,
  categories = NULL,
  ...
)

Arguments

intervals	misha intervals set. Can have an additional 'name' and 'score' fields. When 'type' equals to 'barChart', the intervals should have also a 'strand', 'category' and 'name2' fields.
file	name of the output file
name	track name
type	track type. See https://genome.ucsc.edu/FAQ/FAQformat.html
description	track description
color	color of the track in the genome browser
rm_intervalID	remove intervalID column from intervals
append	append to an existing file
span	span parameter for type = "wig"
categories	categories order for 'barChart' type
...	list of additional attributes such as group or priority. See: https://genome.ucsc.edu/goldenPath/help/customTrack.html

Examples

## Not run: 
gset_genome("mm9")
intervals <- gintervals(1, c(3025716, 3052742, 3181668), c(3026216, 3053242, 3182168))
intervals$score <- c(0.2, 0.5, 1)
fwrite_ucsc(intervals, "out.ucsc",
    name = "clust1", type = "bedGraph",
    graphType = "bar", color = "red", viewLimits = "0:1",
    autoScale = "off"
)
intevals2 <- gintervals(1, c(3671488, 3903482, 3943609), c(3671988, 3903982, 3944109))
intevals2$score <- c(1, 0.2, 0.45)
fwrite_ucsc(intervals2, "out.ucsc",
    name = "clust2", type = "bedGraph",
    graphType = "bar", color = "blue", viewLimits = "0:1",
    autoScale = "off", append = TRUE
)

## End(Not run)

tanaylab/misha.ext documentation built on Oct. 1, 2024, 10:55 a.m.