readIntensities {arrayMagic} | R Documentation |
The function takes the data.frame
slideDescription
as input and reads
the listed image analysis raw data files of
the column slideNameColumn
; cf.
function readpDataSlides
. Each
image analysis raw data file must contain
tab separated columns and a header line -
not necessarily at the top of the file; cf.
the arguments removePatterns
and
skip
. Each file may only contain the
information for one channel, cf. argument
channelColumn
.
The raw data information is returned as an
object of class arrayData
.
Note: All image analysis quantification
(=raw data) files have to correspond
to the same type of microarray.
readIntensities(slideDescription, fileNameColumn="fileName", slideNameColumn, channelColumn = NULL, loadPath=".", type = "GenePix", spotAnnoColumns = NULL, dataColumns = NULL, removePatterns = NULL, skip = NULL, spotIdentifier, ..., verbose = TRUE)
slideDescription |
data.frame ; required; default: missing.
(cf. the return value of the function readpDataSlides )
The data.frame must contain at least one column;
this column has to be named as the argument fileNameColumn .
It may additionally contain a column named slideNameColumn .
|
fileNameColumn |
character string; required; default: "fileName".
fileNameColumn specifies the column which
contains all image quantification result files
in the data.frame of argument
slideDescription . |
slideNameColumn |
character string; optional; default missing;
refers to the data.frame of argument slideDescription .
If slideNameColumn is missing the value is set
to fileNameColumn . |
channelColumn |
named vector of character strings;
optional; default NULL .
If the data.frame of argument
slideDescription contains information
for each channel of every slide/hybridisation separately, the
channelColumn vector contains the column name of the
data.frame of argument slideDescription
used to specify the channel.
If length(channelColumn) == 1 the character strings
"green" and "red" are assumed to be used for the coding,
otherwise names(channelColumn) must contain:
c("channelColumnName","green","red") .
|
loadPath |
character string; required; default: ".". The path is used to load the image quantification result files; note: "." refers to the working directory. |
spotIdentifier |
character string; optional; default missing.
spotIdentifier specifies the column
in the image analysis result files which contain
spot or gene identifiers. |
type |
character string; required;
possible values: "GenePix", "ScanAlyze",
"generic" and "genericOneFilePerChannel";
cf. Details section.
Note: value "generic" requires the arguments
spotAnnoColumns , dataColumns
and possibly skip and removePatterns ,
value "genericOneFilePerChannel" additionally requires
the argument "channelColumn";
whereas "GenPix"
and "ScanAlyze" use predefined values if not
otherwise specified;
default: "GenePix". |
spotAnnoColumns |
vector of character strings;
the column names of the image analysis data file.
The columns must contain the same information for all
files, e.g. the information on the layout of the microarray.
The argument spotIdentifier is automatically
added to the vector if not already included; default: NULL |
dataColumns |
named vector of character strings;
the column names of the image analysis data file.
The columns contain the raw intensities values of each spot;
names(dataColumns) must contain:
c("greenForeground", "greenBackground",
"redForeground", "redBackground") ;
default: NULL
|
removePatterns |
vector of character string(s) each defining
a regular expression; default: NULL ;
all lines of each image analysis raw data file,
which match any of the regular expression(s) are discarded.
|
skip |
integer; default: NULL ;
number of lines skipped in each image analysis data file;
Argument skip applies after all lines matched by
one of the arguments of
removePatterns have been discarded.
|
... |
further arguments which are passed to read.table .
A function which is used inside this function. The arguments
must not include sep , header , as.is
and skip (for skip cf. above).
|
verbose |
logical; required; default TRUE |
Details on the argument type
:
type="GenePix"
defines
spotAnnoColumns = c("Block", "Column", "Row", "Name", "ID")
and
dataColumns = c("F532.Median", "B532.Median",
"F635.Median", "B635.Median")
and corresponding
names(dataColumns) = c("greenForeground", "greenBackground",
"redForeground", "redBackground")
, a dynamically determined argument
skip = grep("Block...Column", imageFile) - 1
and
removePatterns = NULL
,
whereas
type="ScanAlyze"
defines
spotAnnoColumns = c( "HEADER", "SPOT", "GRID", "ROW", "COL" )
and
dataColumns = c("CH1I", "CH1B", "CH2I", "CH2B")
and corresponding
names(dataColumns) = c("greenForeground", "greenBackground",
"redForeground", "redBackground")
,
skip = 0
and
removePatterns = c("^REMARK")
.
object of class arrayData
Andreas Buness <a.buness@dkfz.de>
readpDataSlides
,
arrayData-class