recalculate_expression: Recalculate collapsing probes to genes

In ddeweerd/MODifieRDev: MODifieRDev

Description

Recalculate collapsing probes to genes

Usage

recalculate_expression(MODifieR_input, method)

Arguments

MODifieR_input

A MODifieR input object produced by one of the create_input functions

method

character string for determining which method is used to choose a probe among exactly 2 corresponding rows or when connectivityBasedCollapsing=FALSE. These are the options: "MaxMean" (default) or "MinMean" = choose the row with the highest or lowest mean value, respectively. "maxRowVariance" = choose the row with the highest variance (across the columns of datET). "absMaxMean" or "absMinMean" = choose the row with the highest or lowest mean absolute value. "ME" = choose the eigenrow (first principal component of the rows in each group). Note that with this method option, connectivityBasedCollapsing is automatically set to FALSE. "Average" = for each column, take the average value of the rows in each group "function" = use this method for a user-input function (see the description of the argument "methodFunction"). Note: if method="ME", "Average" or "function", the output parameters "group2row" and "selectedRow" are not informative.

Details

Recalculate the collapsing of probes to genes using on the method options

Value

MODifieR_input object

Author(s)

Dirk de Weerd

See Also

create_input

ddeweerd/MODifieRDev documentation built on Nov. 12, 2019, 7:50 a.m.