pint.data: Forms a data set and pairs samples in two data sets.

In pint: Pairwise INTegration of functional genomics data

Description

Forms a data set for use in functions in 'pint' package (e.g. screen.cgh.mrna). Pairs samples in two data sets.

Usage

pint.data(data, info, impute = TRUE, replace.inf = TRUE, remove.duplicates)
pint.match(X, Y, max.dist = 1e7, chrs = NULL, useSegmentedData =
FALSE, impute = TRUE, replace.inf = TRUE, remove.duplicates = TRUE)

Arguments

data	Probe-level data in a matrix or data frame.
info	Location, chromosome, and chromosome arm. Information of the probes as data frame. Location can be given either as loc or bp, which is middle location of probe, or as start and end. Chromosome arm is given as arm and chromosome as chr.
X, Y	Data sets to be paired.
max.dist	maximum distance between paired genes in base pairs.
chrs	Use to pick a subset of chromosomes in the data. By default, all chromosomes will be used.
useSegmentedData	Logical. If FALSE, rows with identical data are removed (option for pint.match)
remove.duplicates	Logical. If TRUE, rows with identical data are removed (in pint.data), or duplicate signals from many-to-one matches are removed (in pint.match)
impute	Logical. If TRUE, missing values are imputed by replacing them with random samples from a Gaussian distribution following the mean and standard deviation of the non-missing data points from the same sample.
replace.inf	Logical. If TRUE, replace infinite values with highest non-infinite values seen in the data. Otherwise the calculation will halt.

Details

Function pint.match goes through every sample in X and finds the nearest sample in Y which is in the same chromosome arm. If more than one sample in X has same nearest sample in Y, all but one is discarded. Samples with longer distance than max.dist are discarded.

Value

pint.data returns a list with a matrix with sample data and a data frame with chr (chromosome), arm (chromosome arm) and loc (location).

pint.match return a list with two data sets. These can be used in screen.cgh.mrna function.

Author(s)

Olli-Pekka Huovilainen [e-mail]

See Also

screen.cgh.mrna, screen.cgh.mir, fit.cgh.mir.byname

Examples

data(chromosome17)

newData <- pint.match(geneExp,geneCopyNum,max.dist=1000)

pint documentation built on Oct. 31, 2019, 2:41 a.m.