subColSummarize: Summarize columns when divided into groups of rows

In preprocessCore: A collection of pre-processing functions

Description

These functions summarize columns of a matrix when the rows of the matrix are classified into different groups

Usage

subColSummarizeAvg(y, group.labels)
       subColSummarizeAvgLog(y, group.labels)
       subColSummarizeBiweight(y, group.labels)
       subColSummarizeBiweightLog(y, group.labels)
       subColSummarizeLogAvg(y, group.labels)
       subColSummarizeLogMedian(y, group.labels)
       subColSummarizeMedian(y, group.labels)
       subColSummarizeMedianLog(y, group.labels)
       subColSummarizeMedianpolish(y, group.labels)
       subColSummarizeMedianpolishLog(y, group.labels)
       convert.group.labels(group.labels)

Arguments

y	A numeric matrix
group.labels	A vector to be treated as a factor variable. This is used to assign each row to a group. NA values should be used to exclude rows from consideration

Details

These functions are designed to summarize the columns of a matrix where the rows of the matrix are assigned to groups. The summarization is by column across all rows in each group.

• subColSummarizeAvgSummarize by taking mean

• subColSummarizeAvgLoglog2 transform the data and then take means in column-wise manner

• subColSummarizeBiweightUse a one-step Tukey Biweight to summarize columns

• subColSummarizeBiweightLoglog2 transform the data and then use a one-step Tukey Biweight to summarize columns

• subColSummarizeLogAvgSummarize by taking mean and then taking log2

• subColSummarizeLogMedianSummarize by taking median and then taking log2

• subColSummarizeMedianSummarize by taking median

• subColSummarizeMedianLoglog2 transform the data and then summarize by taking median

• subColSummarizeMedianpolishUse the median polish to summarize each column, by also using a row effect (not returned)

• subColSummarizeMedianpolishLoglog2 transform the data and then use the median polish to summarize each column, by also using a row effect (not returned)

Value

A matrix containing column summarized data. Each row corresponds to data column summarized over a group of rows.

Author(s)

B. M. Bolstad <[e-mail]>

Examples

### Assign the first 10 rows to one group and
### the second 10 rows to the second group
###
y <- matrix(c(10+rnorm(50),20+rnorm(50)),20,5,byrow=TRUE)

subColSummarizeAvgLog(y,c(rep(1,10),rep(2,10)))
subColSummarizeLogAvg(y,c(rep(1,10),rep(2,10)))
subColSummarizeAvg(y,c(rep(1,10),rep(2,10)))

subColSummarizeBiweight(y,c(rep(1,10),rep(2,10)))
subColSummarizeBiweightLog(y,c(rep(1,10),rep(2,10)))

subColSummarizeMedianLog(y,c(rep(1,10),rep(2,10)))
subColSummarizeLogMedian(y,c(rep(1,10),rep(2,10)))
subColSummarizeMedian(y,c(rep(1,10),rep(2,10)))



subColSummarizeMedianpolishLog(y,c(rep(1,10),rep(2,10)))
subColSummarizeMedianpolish(y,c(rep(1,10),rep(2,10)))

preprocessCore documentation built on Jan. 10, 2021, 2:01 a.m.