subColSummarize {preprocessCore} | R Documentation |
Summarize columns when divided into groups of rows
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 |
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
subColSummarizeAvgLog
log2
transform the data and then take means in column-wise mannersubColSummarizeBiweightUse a one-step Tukey Biweight to summarize columns
subColSummarizeBiweightLog
log2
transform the data and then use a one-step Tukey Biweight to summarize columnssubColSummarizeLogAvgSummarize by taking mean and then taking
log2
subColSummarizeLogMedianSummarize by taking median and then taking
log2
subColSummarizeMedianSummarize by taking median
subColSummarizeMedianLog
log2
transform the data and then summarize by taking mediansubColSummarizeMedianpolishUse the median polish to summarize each column, by also using a row effect (not returned)
subColSummarizeMedianpolishLog
log2
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 <bmb@bmbolstad.com>
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)))