Type: Package
Title: Tidy Verbs for Dealing with Genomic Data Frames
Version: 0.1.2
Description: Handle genomic data within data frames just as you would with 'GRanges'. This packages provides method to deal with genomic intervals the "tidy-way" which makes it simpler to integrate in the the general data munging process. The API is inspired by the popular 'bedtools' and the genome_join() method from the 'fuzzyjoin' package.
URL: https://github.com/const-ae/tidygenomics
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: dplyr, rlang, purrr, tidyr, fuzzyjoin (≥ 0.1.3), IRanges, Rcpp
Suggests: testthat, knitr, rmarkdown
RoxygenNote: 6.1.1
LinkingTo: Rcpp
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2019-08-08 11:42:50 UTC; ahlmanne
Author: Constantin Ahlmann-Eltze ORCID iD [aut, cre], Stan Developers [cph] (Code from the Stan Math library is reused in 'cluster_interval.cpp'), David Robinson [cph] (Code from the fuzzyjoin package is reused)
Maintainer: Constantin Ahlmann-Eltze <artjom31415@googlemail.com>
Repository: CRAN
Date/Publication: 2019-08-08 11:50:02 UTC

Cluster ranges which are implemented as 2 equal-length numeric vectors.

Description

Cluster ranges which are implemented as 2 equal-length numeric vectors.

Usage

cluster_interval(starts, ends, max_distance = 0L)

Arguments

starts

A numeric vector that defines the starts of each interval

ends

A numeric vector that defines the ends of each interval

max_distance

The maximum distance up to which intervals are still considered to be the same cluster. Default: 0.

Examples

starts <- c(50, 100, 120)
ends <- c(75, 130, 150)
j <- cluster_interval(starts, ends)
j == c(0,1,1)

Intersect data frames based on chromosome, start and end.

Description

Intersect data frames based on chromosome, start and end.

Usage

genome_cluster(x, by = NULL, max_distance = 0,
  cluster_column_name = "cluster_id")

Arguments

x

A dataframe.

by

A character vector with 3 entries which are the chromosome, start and end column. For example: by=c("chr", "start", "end")

max_distance

The maximum distance up to which intervals are still considered to be the same cluster. Default: 0.

cluster_column_name

A string that is used as the new column name

Value

The dataframe with the additional column of the cluster

Examples


library(dplyr)

x1 <- data.frame(id = 1:4, bla=letters[1:4],
                 chromosome = c("chr1", "chr1", "chr2", "chr1"),
                 start = c(100, 120, 300, 260),
                 end = c(150, 250, 350, 450))
genome_cluster(x1, by=c("chromosome", "start", "end"))
genome_cluster(x1, by=c("chromosome", "start", "end"), max_distance=10)

Calculates the complement to the intervals covered by the intervals in a data frame. It can optionally take a chromosome_size data frame that contains 2 or 3 columns, the first the names of chromosome and in case there are 2 columns the size or first the start index and lastly the end index on the chromosome.

Description

Calculates the complement to the intervals covered by the intervals in a data frame. It can optionally take a chromosome_size data frame that contains 2 or 3 columns, the first the names of chromosome and in case there are 2 columns the size or first the start index and lastly the end index on the chromosome.

Usage

genome_complement(x, chromosome_size = NULL, by = NULL)

Arguments

x

A data frame for which the complement is calculated

chromosome_size

A dataframe with at least 2 columns that contains first the chromosome name and then the size of that chromosome. Can be NULL in which case the largest value per chromosome from x is used.

by

A character vector with 3 entries which are the chromosome, start and end column. For example: by=c("chr", "start", "end")

Examples


library(dplyr)

x1 <- data.frame(id = 1:4, bla=letters[1:4],
                 chromosome = c("chr1", "chr1", "chr2", "chr1"),
                 start = c(100, 200, 300, 400),
                 end = c(150, 250, 350, 450))

genome_complement(x1, by=c("chromosome", "start", "end"))

Intersect data frames based on chromosome, start and end.

Description

Intersect data frames based on chromosome, start and end.

Usage

genome_intersect(x, y, by = NULL, mode = "both")

Arguments

x

A dataframe.

y

A dataframe.

by

A character vector with 3 entries which are used to match the chromosome, start and end column. For example: by=c("Chromosome"="chr", "Start"="start", "End"="end")

mode

One of "both", "left", "right" or "anti".

Value

The intersected dataframe of x and y with the new boundaries.

Examples


library(dplyr)

x1 <- data.frame(id = 1:4, bla=letters[1:4],
                 chromosome = c("chr1", "chr1", "chr2", "chr2"),
                 start = c(100, 200, 300, 400),
                 end = c(150, 250, 350, 450))

x2 <- data.frame(id = 1:4, BLA=LETTERS[1:4],
                 chromosome = c("chr1", "chr2", "chr2", "chr1"),
                 start = c(140, 210, 400, 300),
                 end = c(160, 240, 415, 320))
j <- genome_intersect(x1, x2, by=c("chromosome", "start", "end"), mode="both")
print(j)

Join intervals on chromosomes in data frames, to the closest partner

Description

Join intervals on chromosomes in data frames, to the closest partner

Usage

genome_join_closest(x, y, by = NULL, mode = "inner",
  distance_column_name = NULL, max_distance = Inf, select = "all")

genome_inner_join_closest(x, y, by = NULL, ...)

genome_left_join_closest(x, y, by = NULL, ...)

genome_right_join_closest(x, y, by = NULL, ...)

genome_full_join_closest(x, y, by = NULL, ...)

genome_semi_join_closest(x, y, by = NULL, ...)

genome_anti_join_closest(x, y, by = NULL, ...)

Arguments

x

A dataframe.

y

A dataframe.

by

A character vector with 3 entries which are used to match the chromosome, start and end column. For example: by=c("Chromosome"="chr", "Start"="start", "End"="end")

mode

One of "inner", "full", "left", "right", "semi" or "anti".

distance_column_name

A string that is used as the new column name with the distance. If NULL no new column is added.

max_distance

The maximum distance that is allowed to join 2 entries.

select

A string that is passed on to IRanges::distanceToNearest, can either be all which means that in case that multiple intervals have the same distance all are reported, or arbitrary which means in that case one would be chosen at random.

...

Additional arguments parsed on to genome_join_closest.

Value

The joined dataframe of x and y.

Examples


library(dplyr)

x1 <- data.frame(id = 1:4, bla=letters[1:4],
                 chromosome = c("chr1", "chr1", "chr2", "chr2"),
                 start = c(100, 200, 300, 400),
                 end = c(150, 250, 350, 450))

x2 <- data.frame(id = 1:4, BLA=LETTERS[1:4],
                 chromosome = c("chr1", "chr2", "chr2", "chr1"),
                 start = c(140, 210, 400, 300),
                 end = c(160, 240, 415, 320))
j <- genome_intersect(x1, x2, by=c("chromosome", "start", "end"), mode="both")
print(j)

Subtract one data frame from another based on chromosome, start and end.

Description

Subtract one data frame from another based on chromosome, start and end.

Usage

genome_subtract(x, y, by = NULL)

Arguments

x

A dataframe.

y

A dataframe.

by

A character vector with 3 entries which are used to match the chromosome, start and end column. For example: by=c("Chromosome"="chr", "Start"="start", "End"="end")

Value

The subtracted dataframe of x and y with the new boundaries.

Examples


library(dplyr)

x1 <- data.frame(id = 1:4, bla=letters[1:4],
                 chromosome = c("chr1", "chr1", "chr2", "chr1"),
                 start = c(100, 200, 300, 400),
                 end = c(150, 250, 350, 450))

x2 <- data.frame(id = 1:4, BLA=LETTERS[1:4],
                 chromosome = c("chr1", "chr2", "chr1", "chr1"),
                 start = c(120, 210, 300, 400),
                 end = c(125, 240, 320, 415))

j <- genome_subtract(x1, x2, by=c("chromosome", "start", "end"))
print(j)