mkatari-bioinformatics-august-2013-loadingphytozome
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mkatari-bioinformatics-august-2013-loadingphytozome [2013/08/21 09:34] – mkatari | mkatari-bioinformatics-august-2013-loadingphytozome [2015/06/18 09:05] – mkatari | ||
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===== Read Phytozome annotation file. ===== | ===== Read Phytozome annotation file. ===== | ||
- | This step was tricky because there were characters such as quotes and hash marks. We need to reset the default values to allow the file to load without a problem. | + | This step was tricky because there were characters such as quotes and hash marks. We need to reset the default values to allow the file to load without a problem. |
< | < | ||
- | anno< | + | anno< |
| | ||
| | ||
Line 25: | Line 25: | ||
===== Run Fisher Exact Test ===== | ===== Run Fisher Exact Test ===== | ||
- | Start by sourcing | + | Let's use the significant genes identified from Deseq as our example. |
< | < | ||
- | gene.list< | + | |
+ | gene.list< | ||
</ | </ | ||
- | The function itself is called doFisherTest. It has three arguments: gene.list, gene2go , and go2gene. The last two use gene2go and go2gene as default but different lists can be provided here. | + | Start by sourcing the [[https:// |
To run the function: | To run the function: | ||
< | < | ||
- | goresults=doFisherTest(gene.list) | + | source(" |
+ | goterm_annot< | ||
+ | row.names=1, | ||
+ | goresults=doFisherTest(as.character(gene.list[,1]), goAnnot=goterm_annot) | ||
+ | write.table(goresults, | ||
</ | </ | ||
+ | |||
+ | Visualizing your results in the GO-term graph. Use the RamiGO package. Simply provide the GO terms that are enriched and the corresponding p-value for the go-terms. By default it will save a file to your working directory called RamiGO.png | ||
+ | |||
+ | < | ||
+ | source(" | ||
+ | biocLite(" | ||
+ | library(RamiGO) | ||
+ | getAmigoTree(rownames(gotermresults)[1: | ||
+ | </ | ||
+ |
mkatari-bioinformatics-august-2013-loadingphytozome.txt · Last modified: 2015/06/18 09:05 by mkatari