plot_ES_score: re-draw ES-score figures for GSEA
In jmzeng1314/humanid: gene id annotation

Description Usage Arguments Value Examples

It's very complicate,please don't use this unless you have a clear understanding of the mechanism for the GSEA especially for the ES core ,the running ES core, the gene sets ! you need to prepare many data by yourself, I really can't help you with them. #'

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plot_ES_score(imageType = "png", width = 680, height = 680, res = 200,
  Ng = 12, N = 34688, phen1 = "control", phen2 = "case", Obs.RES,
  Obs.indicator, obs.s2n, size.G, gs.names, Obs.ES, Obs.arg.ES, Obs.ES.index)

`imageType`	choose png,pdf,emf,tiff,jpeg,bmp
`Ng`	The number of the gene sets, (eg: 200~300 kegg pathway)
`N`	The number of the genes (probably 20,000~30,000 genes)
`phen1`	The name for the first phenotype (default:control)
`phen2`	The name for the second phenotype (default:case)
`Obs.RES`	A matrix, running ES score for each gene in specific gene Set.
`Obs.indicator`	A matrix, 0/1 shows whether a gene belong to a gene Set.
`obs.s2n`	A vector of sigal to noise value for each gene (sorted, and Z-score)
`size.G`	A vector for the size of each geneSet
`gs.names`	A vector for the name of each geneSet
`Obs.ES`	A vector for the maximal ES score of each gene Set.
`Obs.arg.ES`	A vector for the order of the gene shows maximal ES score of each gene Set.

write some files

1	#' plot_ES_score(imageType='png',width = 680,height = 680 ,Ng=12,N=34688,phen1='Control',phen2='case',Obs.RES,Obs.indicator,obs.s2n,size.G,gs.names,Obs.ES,Obs.arg.ES,Obs.ES.index)

jmzeng1314/humanid documentation built on May 19, 2019, 2:57 p.m.