Description Usage Arguments Examples
This function creates a number of new AGSs from a given dataset, such as gene copy number, gene/protein expression, gene methylation etc. Such matrices M typically have size Ngenes x Nsamples, so that the current function returns a list of length=ncol(M)
. The AGSs for each of the Nsamples are created with one of the five available methods (see parameter method
).
1 2 3 | samples2ags(m0, Ntop = NA, col.mask = NA, namesFromColumn = NA,
method = c("significant", "top", "toppos", "topnorm", "bestp", "toprandom"),
cutoff.q = 0.05)
|
m0 |
input matrix. |
Ntop |
Number of top ranking genes to include into each sample-specific AGS. Mutually exclusive with "cutoff.q". A practically recommended value of Ntop could be in the range 30...300. Ntop>1000 might decrease the analysis specificity. |
col.mask |
To include only columns with IDs that contain the specified mask. Follows the regular expression syntax. |
namesFromColumn |
Number of the column (if any) that contains the gene/protein names. Note that it is only necessary of the latter are NOT the unique rownames of the matrix. This could be sometimes needed to be able to process redundant expression etc. profiles. |
method |
Method to select sample-specific genes. One of
|
cutoff.q |
cutoff value. Mutually exclusive with "Ntop" (default: 0.05) |
1 2 | data("fantom5.43samples", package="NEArender")
ags.list <- samples2ags(fantom5.43samples, cutoff.q = 0.01, method="significant")
|
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