Calculate Means \& Standard Deviations of Intensities

Description

Function to calculate the mean and standard deviation of the intensity for each chromosome for each scan.

Usage

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meanIntensityByScanChrom(intenData, vars = c("X", "Y"), 
                         snp.exclude = NULL, verbose = TRUE)

Arguments

intenData

IntensityData object. Chromosomes are expected to be in contiguous blocks.

vars

Character vector with the names of one or two intensity variables.

snp.exclude

An integer vector containing SNPs to be excluded.

verbose

Logical value specifying whether to show progress information.

Details

The names of two intensity variables in intenData may be supplied. If two variables are given, the mean of their sum is computed as well. The default is to compute the mean and standard deviation for X and Y intensity.

Value

A list with two components for each variable in "vars": 'mean.var' and 'sd.var'. If two variables are given, the first two elements of the list will be mean and sd for the sum of the intensity variables:

mean.intensity

A matrix with one row per scan and one column per chromosome containing the means of the summed intensity values for each scan and chromosome.

sd.intensity

A matrix with one row per scan and one column per chromosome containing the standard deviations of the summed intensity values for each scan and chromosome.

mean.var

A matrix with one row per scan and one column per chromosome containing the means of the intensity values for each scan and chromosome.

sd.var

A matrix with one row per scan and one column per chromosome containing the standard deviations of the intensity values for each scan and chromosome.

Author(s)

Cathy Laurie

See Also

IntensityData, mean, sd

Examples

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file <- system.file("extdata", "illumina_qxy.gds", package="GWASdata")
gds <- GdsIntensityReader(file)
intenData <- IntensityData(gds)

meanInten <- meanIntensityByScanChrom(intenData)
close(intenData)

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