GSload.genelist {GeneSpring}R Documentation

Load and save GeneSpring gene lists

Description

These functions load and save list of genes from and to GeneSpring. Gene lists can consists of a simple list of genes or can contain one column of associtated values containing either the classifications or some numeric value representing the result of an analysis (Like P values after a ANOVA for instance).

Usage

glist <- GSload.genelist(filename = "GS_R_in.txt")
GSsave.genelist(genelist, filename = "GS_R_out.txt")

Arguments

filename Name of the file of the genelist. Can be connection object like stdin().
genelist Gene list to be saved to the file. Can either be a list or a data frame/matrix.

Details

Gene lists are either simple lists or vectors of gene names or data.frames. When the gene list contains associated values, the gene list is stored as a data.frame, with the gene names as the row.names of the data.frame and the values in the first (and only) column of the data.frame.

There are two types of gene lists within GeneSpring, although only one is actually called a gene lists while the other one is called a classification.

Gene lists proper are list of genes in GeneSpring with an optional NUMERICAL associated value. This numerical values usually represents the result of one or more analyses, like the P value of an ANOVA, or the number of samples that passed the filter that was applied.

The other type of gene lists are those lists that are produced when a Classification is saved to a file. The classification objects are the result of the clustering methods in GeneSpring, like K-means clustering or the QT-clustering. When classifications are stored in file from GeneSpring, the classifications are simply gene lists with STRING associated values, where the values designate the cluster name that gene belongs to.

The two functions GSload.genelist and GSsave.genelist will not make a distinction between the two types of gene lists and it is left to the user to determine from the contents of the genelists which of the two types has been loaded.

When a classification is attempted to be loaded into GeneSpring as a proper gene list, the associated values will simply be missing if they are non-numerical.

Value

The GSload.genelist() function will return either a vector of genenames, if the input was a simple list of genes, or a data.frame where the gene names are the row names and one column of associated data.

Note

This and any other functions in the GeneSpring package are only useful, when using Agilent Technologies Gene Expression software GeneSpring.

Author(s)

Thon de Boer, Agilent Technologies, Santa Clara, CA, USA thon_deboer@agilent.com

References

For more information on using GeneSpring with R see http://www.silicongenetics.com/cgi/SiG.cgi/Support/GeneSpring/GSnotes/R.smf

See Also

Examples

#Create a simple GeneList
glist <- c("160640_at","101906_at", "104099_at")
#Save the genelist to a file
GSsave.genelist(glist, filename = "GS_R_out.txt")
#Load the genelist again
g2 <- GSload.genelist(filename = "GS_R_out.txt")
#Add some values to the genelist as associated values by making a data.frame out of it
g3 <- data.frame(value=rnorm(3), row.names = g2)
#Save the genelist again to the default file ("GS_R_out.txt")
GSsave.genelist(g3)
#Load the gene list and display
GSload.genelist(filename = "GS_R_out.txt")

#Create classification style gene list
g4 <- data.frame(classification=c("Cluster 1","Cluster 2", "Cluster 1"), row.names = g2)
GSsave.genelist(g4)
#Load the gene list and display
GSload.genelist(filename = "GS_R_out.txt")


[Package GeneSpring version 2.0.0 Index]