transcriptogramStep1 {transcriptogramer} | R Documentation |
For each transcriptome sample, this method assigns to each protein the
average of the expression values of all the identifiers related to
it. It is necessary a
dictionary
to map the identifiers to proteins.
transcriptogramStep1(object, expression, dictionary, nCores = 1L) ## S4 method for signature 'Transcriptogram' transcriptogramStep1(object, expression, dictionary, nCores = 1L)
object |
An object of class Transcriptogram. |
expression |
A matrix, or data.frame, containing normalized expression values from samples of microarrays or RNA-Seq (log2-counts-per-million). |
dictionary |
A matrix, or data.frame, containing two columns, the first
column must contains the
ENSEMBL Peptide ID, and the second column must contains values that appear
as rownames in |
nCores |
An integer number, referring to the number of processing cores to be used; or a logical value, TRUE indicating that all processing cores should be used, and FALSE indicating the use of just one processing core. The default value of this argument is 1. |
This method creates a data.frame to feed the transcriptogramS1 slot of an object of class Transcriptogram. Each row of the data.frame contains: an ENSEMBL Peptide ID, its respective position in the ordering and the mean of the expression values of the identifiers related to the same protein.
Diego Morais
da Silva, S. R. M., Perrone, G. C., Dinis, J. M., and de Almeida, R. M. C. (2014). Reproducibility enhancement and differential expression of non predefined functional gene sets in human genome. BMC Genomics.
Rybarczyk-Filho, J. L., Castro, M. A. A., Dalmolin, R. J. S., Moreira, J. C. F., Brunnet, L. G., and de Almeida, R. M. C. (2011). Towards a genome-wide tran-scriptogram: the Saccharomyces cerevisiae case. Nucleic Acids Research, 39(8), 3005-3016.
transcriptogramPreprocess, GSE9988, GPL570, Hs900, association
transcriptogram <- transcriptogramPreprocess(association, Hs900) ## Not run: transcriptogram <- transcriptogramStep1(transcriptogram, GSE9988, GPL570) ## End(Not run)