summarizeReplicates {maigesPack} | R Documentation |
Function to summarise measures of a maiges
class object,
both by samples and genes.
summarizeReplicates(object=NULL, gLabelID="GeneName", sLabelID="Sample", funcS="mean", funcG="mean", rmBad=TRUE, keepEmpty=TRUE)
object |
object of class maiges . |
gLabelID |
character string giving the gene label ID to be used to summarise the data by rows. |
sLabelID |
character string giving the sample label ID to be used to summarise the data by columns. |
funcS |
character string specifying the function to be applied for sample replicates. Defaults to 'mean'. If NULL, no resume is done for samples. |
funcG |
character string specifying the function to be applied for genes (spots) replicates. Defaults to 'mean'. If NULL, no resume is done for genes.. |
rmBad |
logical indicating if you want to remove or not bad
spots, given by the slot BadSpots in argument object . |
keepEmpty |
logical indicating if you want to maintain spots with empty information. |
This function takes the object of class maiges
and
resume the data by spots (rows) and samples (columns).
This function returns another object of class maiges
with replicates summarised to only one observation.
Gustavo H. Esteves <gesteves@vision.ime.usp.br>
## Loading the dataset data(gastro) ## Summarising the data (maigesNorm class), replicated samples will be ## summarised by mean and genes by median gastro.summ = summarizeReplicates(gastro.norm, gLabelID="GeneName", sLabelID="Sample", funcS="mean", funcG="median", keepEmpty=FALSE, rmBad=FALSE) ## To summarise genes by mean and keep the blank spots use gastro.summ = summarizeReplicates(gastro.norm, gLabelID="GeneName", sLabelID="Sample", funcS="mean", funcG="mean", keepEmpty=TRUE, rmBad=FALSE)