Determine the type (or status) of each spot in the gene list.
dataframe containing spot type specifiers, usually input using
dataframe containing gene annotation, or an object of class
integer or name specifying column of
vector of integers or column names specifying columns of types containing regular expressions.
Defaults to any column names in common between
This function constructs a vector of status codes by searching for patterns in the gene list.
The data frame
genes contains gene IDs and should have as many rows as there are spots on the microarrays.
Such a data frame is often read using
The data frame
types has as many rows as you want to distinguish types of spots in the gene list.
This data frame should contain a column or columns, the
regexpcol columns, which have the same names as columns in
genes and which contain patterns to match in the gene list.
Another column, the
spottypecol, contains the names of the spot types.
Any other columns are assumed to contain plotting parameters, such as colors or symbols, to be associated with the spot types.
The patterns in the
regexpcol columns are simplified regular expressions.
AA* means any string starting with
*AA means any code ending with
AA means exactly these two letters,
*AA* means any string containing
AA followed by exactly one other character and
AA\. means exactly
AA followed by a period and no other characters.
Any other regular expressions are allowed but the codes
^ for beginning of string and
$ for end of string should not be included.
Note that the patterns are matched sequentially from first to last, so more general patterns should be included first.
For example, it is often a good idea to include a default spot-type as the first line in
types with pattern
* for all
regexpcol columns and default plotting parameters.
Character vector specifying the type (or status) of each spot on the array. Attributes contain plotting parameters associated with each spot type.
An overview of LIMMA functions for reading data is given in 03.ReadingData.
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genes <- data.frame( ID=c("Control","Control","Control","Control","AA1","AA2","AA3","AA4"), Name=c("Ratio 1","Ratio 2","House keeping 1","House keeping 2", "Gene 1","Gene 2","Gene 3","Gene 4")) types <- data.frame( SpotType=c("Gene","Ratio","Housekeeping"), ID=c("*","Control","Control"), Name=c("*","Ratio*","House keeping*"), col=c("black","red","blue")) status <- controlStatus(types,genes)
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