getprobes {phyloarray}R Documentation

Adding probes to object

Description

Reads the for each "Probename", all match and mismatch probes from a .csv-file. The fields are normally delimited with a comma, and the fields surroundend by quotes.

Usage

  getprobes(datalist, file, header=T, sep=",", quote="\"", fill=T, ...)

Arguments

datalist An object of type phyloarray
file The file to be read
header The first row should contain the columns names. The first columns should be named "Probename". The following columns may have any name, and the user should use these names for further analysis.
sep The delimiter between field. Standard value is a comma.
quote The quotes around the field values.
fill If the number of columns is unequal, blank fields are added.
... Additional parameters for read.csv

Value

An object of class phyloarray is returned, with attribute probes added. This is a dataframe containing for each probename, several match and mismatch probe ID's.

Note

Author(s)

Kurt Sys (kurt.sys@advalvas.be)

References

See Also

Scandataraw Phylodata

init.data

read.csv

Examples

  # load data this-is-escaped-codenormal-bracket40bracket-normal, i.e. this-is-escaped-codenormal-bracket41bracket-normal
  data(Phylodata)

  # read the probes from a this-is-escaped-codenormal-bracket42bracket-normal-file
  # scans <- getprobes(scans, file="probes.csv")

  # names of the columns
  names(attr(scans, "probes"))

  # the list of probenames and -ID's
  attributes(scans)$probes

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