aCGH.read.Sprocs: Create object of class "aCGH" from Sproc files

Description Usage Arguments Value Author(s) See Also Examples

View source: R/aCGH.read.R

Description

This function reads in two-channel Array Comparative Genomic Hybridization Sproc files, flags them for bad quality and missing data, and creates object of class aCGH.

Usage

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aCGH.read.Sprocs(fnames, latest.mapping.file = NULL, maxsd = 0.2,
                 minreplic = 2, chrom.remove.threshold = 24,
                 prop.missing = 0.25, sample.names = fnames,
                 sample.quality.threshold = 0.4,
                 cols = c("Log2Rat", "Log2StdDev", "NReplic", "Bad.P"),
                 unmapScreen=TRUE, dupRemove = TRUE)

Arguments

fnames

a vector of character strings containing the file names of each Sproc data file.

latest.mapping.file

The name of an optional file that contains newer clone mapping different from the clone mapping used at the time when the arrays were created.

maxsd

maximum of standard deviation of log2 ratios used in pre-filtering.

minreplic

minimum number of replicates per clone for a single chip used to calculate the log2 ratios.

chrom.remove.threshold

Chromosomes are ordered and numbered as usual, except for X and Y chromosome, which in for Homo sapiens genome have numbers 23 and 24 repsectivelly, in for Mus musculus 20 and 21, etc.

prop.missing

Clones are screened out and if the proportion missing in the samples is prop.missing they are removed.

sample.names

Sample names. If they are missing, the file names are used after stripping the characters after the last dot in the filename if one exists; for example 'myfile.txt' becomes myfile.

sample.quality.threshold

Mark those samples that have their proportion of missing values sample.quality.threshold.

cols

character vector of length 4 containing the following Sproc file column names: log2 ratios, std. deviations of the log2 ratios, number of replicates for each clone and flags for bad clones. Defaults to c("Log2Rat", "Log2StdDev", "NReplic", "Bad.P"). Note that all the whitespace characters in the column names will be replaced with dots.

unmapScreen

Indicator for whether clones with incomplete mapping information should be removed from the dataset. Note that leaving them in may cause plotting routines fail. Defaults to TRUE

dupRemove

Indicator for whether clones with duplicate names should be averaged and removed from the dataset leaving only one occurence of each duplicated set.Defaults to TRUE

Value

Object of class aCGH.

Author(s)

Jane Fridlyand, Peter Dimitrov

See Also

aCGH

Examples

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datadir <- system.file("examples", package = "aCGH")
latest.mapping.file <-
      file.path(datadir, "human.clones.info.Jul03.txt")
ex.acgh <-
	aCGH.read.Sprocs(dir(path = datadir,pattern = "sproc",
			full.names = TRUE), latest.mapping.file,
			chrom.remove.threshold = 23)
ex.acgh

## Testing if creating the object went right. Should all be true.

all(log2.ratios(ex.acgh)[ 1, ] == c(-0.077698 , 0.007389))
clone.name <- "HumArray2H10_T30"
all(log2.ratios(ex.acgh)[ clone.name, ] == c(0.025567 , -0.036908))

Bioconductor-mirror/aCGH documentation built on June 1, 2017, 4:13 a.m.