R语言 GSVA包 computeGeneSetsOverlap()函数中文帮助文档(中英文对照)

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computeGeneSetsOverlap(GSVA)
computeGeneSetsOverlap()所属R语言包：GSVA

                                         Compute gene-sets overlap
                                         计算基因组重叠

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Calculates the overlap among every pair of gene-sets given as input.
计算作为输入的每对基因组之间的重叠。


用法----------Usage----------


## S4 method for signature 'list,character'
computeGeneSetsOverlap(gSets, uniqGenes, min.sz=1, max.sz=Inf)
## S4 method for signature 'list,ExpressionSet'
computeGeneSetsOverlap(gSets, uniqGenes, min.sz=1, max.sz=Inf)
## S4 method for signature 'GeneSetCollection,character'
computeGeneSetsOverlap(gSets, uniqGenes, min.sz=1, max.sz=Inf)
## S4 method for signature 'GeneSetCollection,ExpressionSet'
computeGeneSetsOverlap(gSets, uniqGenes, min.sz=1, max.sz=Inf)



参数----------Arguments----------

参数：gSets
Gene sets given either as a list or a GeneSetCollection object.
基因集作为list或GeneSetCollection对象的。


参数：uniqGenes
Vector of unique genes to be considered when calculating the overlaps.
计算的重叠时，被视为独特的基因向量。


参数：min.sz
Minimum size.
最小尺寸。


参数：max.sz
Maximum size.
最大大小。


Details

详情----------Details----------

This function calculates the overlap between every pair of gene sets of the input argument gSets. Before this calculation takes place, the gene sets in gSets are firstly filtered to discard genes that do not match to the identifiers in uniqGenes. Secondly, they are further filtered to meet the minimum and/or maximum size specified with the arguments min.sz and max.sz. The overlap between two gene sets is calculated as the number of common genes between the two gene sets divided by the smallest size of the two gene sets.
此函数计算每双输入参数gSets基因组之间的重叠。计算发生在此之前，该基因设定在gSets首先过滤，丢弃不匹配uniqGenes标识符的基因。其次，他们正在进一步筛选，以满足最小和/或最大规模的论点min.sz和max.sz指定。两个基因组之间的重叠设置分为两个基因组的最小尺寸的共同基因的两个基因之间的数量计算。


值----------Value----------

A gene-set by gene-set matrix of the overlap among every pair of gene sets.
A基因组基因组每对基因组之间的重叠矩阵。


作者（S）----------Author(s)----------


J. Guinney



参考文献----------References----------

GSVA: Gene Set Variation Analysis, submitted

参见----------See Also----------

filterGeneSets
filterGeneSets


举例----------Examples----------



geneSets <- list(set1=as.character(1:4), set2=as.character(4:10))

computeGeneSetsOverlap(geneSets, unique(unlist(geneSets)))


转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。


注：
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