parallelize: Reshapes a list of segments

Description Usage Arguments Value Author(s) See Also

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

1
  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.