python scipy包进行GO富集分析p值计算

最近总是有需要单独对某一个类型的通路进行超几何分布的p值计算，这里记录一下python包的计算方法

使用scipy的stat里面的hypergeom.sf方法进行富集分析的p值计算

hsaxxxxx AA and Linoleic metabolism KEGG pathways Pathways KEGG (Homo sapiens (human)) 59 17 3586 141 3.32E-11

------------ set in set background in background pathway 59 17 3586 141 description k x m+n m

x: the number of white balls drawn without replacement from an urn which contains both black and white balls. m: the number of white balls in the urn n: the number of black balls in the urn k: number of balls drawn from the urn

from scipy import stats
#需要注意的是16是由17-1得到的
stats.hypergeom.sf(16,3586,141, 59)

R中的实现方式

phyper(x, m, n, k, lower.tail=FALSE)

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