ArrayBuildfData: collapse feature data of 'ExpressionSet' object by...
In ShixiangWang/iProfile: integrated cancer Profile using multiple datasets

Description Usage Arguments Details Value Author(s)

This function is used to collapse multiple identifier to unique one by a function

1 2	ArrayBuildfData(exprz = NULL, name = NULL, identifier = c("SYMBOL", "ENTREZ_ID"), collapse_fun = median)

`exprz`	a `ExpressionSet` object. The first column of `fData` of this object is equal to `rownames(exprs(exprz))`, and alWways stores probe IDs.
`name`	a character tells the names of the `ExpressionSet` object. You can treat it as a ID for the `exprz` object.
`identifier`	a character. "SYMBOL" is default to set gene symbols will be the rownames of expression matrix. You can also use "ENTREZ_ID".
`collapse_fun`	a function object used for collapsing multiple identifiers with same name to unique one. NA and "" will be removed.

In expression dataset, we often meet there are multiple probes mapping to one gene id or symbol. While we want make gene expression unique, this function works for this purpose. Due to multiple probes mapping to one gene, the identifier should be "SYMBOL" (gene symbol) or "ENTREZ_ID (entrez id), then collapse_fun function will be called and unique identifiers will substitute probe IDs, unique gene expression value computed by collapse_fun will substitute multiple probe values mapping to one gene.

a ExpressionSet object.

Shixiang Wang <w_shixiang@163.com>

ShixiangWang/iProfile documentation built on May 11, 2019, 6:25 p.m.