parallelize: Reshapes a list of segments

In cghRA: Array CGH Data Analysis and Visualization

Description

This function reshapes a list of segment data.frames (with chromosomal location and value) into a single data.frame containing a column for each element of the list (typically samples) and a the minimal amount of regions in rows.

Usage

  parallelize(segTables, value = "logRatio", digits = 3, quiet = FALSE, chroms = NULL)

Arguments

segTables	An eventually named list of data.frames to reshape. All the data.frames must contain at least "chrom" (character), "start" (integer), "end" (integer) columns, and the column defined by value. Can also be a single data.frame containing all the segments, with a .sampleIdentity integer column.
value	Single character value, the column name from which extract values that will fill the output cells.
digits	Single integer value to be passed to round for each cell of the output (NA disables the rounding step).
quiet	Single logical value, whether to throw diagnosis messages or not.
chroms	Character vector, the names of chromosomes to restrain the analysis on (frequently autosomes). If NULL, all chromosomes in segTable will be used.

Value

Returns a data.frame with the following columns :

chrom	Character, the chromosomal location of the region described.
start	Integer, the lower coordinate of the region described.
end	Integer, the upper coordinate of the region described.
...	For each element of segTables a column with the value extracted from the value column of the according data.frame.

Author(s)

Sylvain Mareschal

See Also

penetrance

cghRA documentation built on May 2, 2019, 3:34 a.m.