[BioC] KEGG pathway heat map

[Felipe Antonio Riveroll Aguirre]

Hi.

Finally I found how to get an input file, for color-KEGG-pathways script.

After following this tutorial
http://gettinggeneticsdone.blogspot.mx/2012/03/pathway-analysis-for-high-throughput.html
you get a list of pathways with highlighted genes, then if you wanna
get a heat map, from SPIA maped genes,  you could use this pyhon
script https://github.com/ajmazurie/color-KEGG-pathways/, but you need
an input with these values, for every gene

KEGG_Pathway_ID,KEGG_obj_ID,value

This is my code, but I dont known how to get the list of the SPIA
pathway linked genes, I do this step manually deleting the web address
and replacing "+" with ", " in a text editor, from the KEGGLINK. Could
you help me to get this with R?

#Genes linked with SPIA result from 1st pathway
hsa04510 <- c(3678, 3680, 2316, 10398, 2534, 1278, 1282, 1293, 5649,
7058, 7148, 7450, 857, 858, 3479, 5155, 7424, 3725)

#Get a subset of logFC values for pathway linked genes
hsa04510.exp <- sig_genes[which(names(sig_genes) %in% hsa04510)]

#Load the results as data frame
hsa04510.df <- as.data.frame(hsa04510.exp)

#Get the first col for the output needed for the python script
color-KEGG-pathways
# https://github.com/ajmazurie/color-KEGG-pathways/blob/master/README.rst
ruta <- rep("hsa04510", length(hsa04510))

#Get the second Col
hsa04510.genes.out <- c(paste("hsa:",names(hsa04510.exp), sep=""))

#Now get the data frame with the required output
hsa04510.color.input <- data.frame (ruta, hsa04510.genes.out, hsa04510.df[[1]])

#Write to a file
write.table(hsa04510.color.input, "hsa04510.color.input.csv", sep=",",
quote=FALSE, row.names = FALSE,
            col.names = FALSE)


Felipe Antonio Riveroll Aguirre, QFB
Departamento de Bioquímica
Laboratorio 26
CINVESTAV, México D. F.
CP 07360
Tel. +52 (55) 5747-3800 ext 5217
Celular. +52 (55) 3351-2251
Sitio web: http://www.feliperiveroll.name



2012/5/3 Felipe Riveroll Aguirre <friveroll at gmail.com>
>
> I am trying to get a KEGG pathway heat map with this python script
> https://github.com/ajmazurie/color-KEGG-pathways/blob/master/README.rst
>