qSig | R Documentation |
qSig
ObjectIt builds a 'qSig' object to store the query signature, reference database and GESS method used for GESS methods.
qSig(query, gess_method, refdb)
query |
If 'gess_method' is 'CMAP' or 'LINCS', it should be a list with
two character vectors named If 'gess_method' is 'gCMAP', the query is a matrix with a single column representing gene ranks from a biological state of interest. The corresponding gene labels are stored in the row name slot of the matrix. Instead of ranks one can provide scores (e.g. z-scores). In such a case, the scores will be internally transformed to ranks. If 'gess_method' is 'Fisher', the query is expected to be a list with two
character vectors named If 'gess_method' is 'Cor', the query is a matrix with a single numeric column and the gene labels in the row name slot. The numeric column can contain z-scores, LFCs, (normalized) gene expression intensity values or read counts. |
gess_method |
one of 'CMAP', 'LINCS', 'gCMAP', 'Fisher' or 'Cor' |
refdb |
character(1), can be one of "cmap", "cmap_expr", "lincs",
"lincs_expr", "lincs2" when using the CMAP/LINCS databases from the affiliated
To use a custom database, it should be the file path to the HDF5
file generated with the When the |
qSig
object
build_custom_db
,
signatureSearchData
,
gmt2h5
, qSig-class
db_path <- system.file("extdata", "sample_db.h5",
package = "signatureSearch")
qsig_lincs <- qSig(query=list(
upset=c("230", "5357", "2015", "2542", "1759"),
downset=c("22864", "9338", "54793", "10384", "27000")),
gess_method="LINCS", refdb=db_path)
qmat <- matrix(runif(5), nrow=5)
rownames(qmat) <- c("230", "5357", "2015", "2542", "1759")
colnames(qmat) <- "treatment"
qsig_gcmap <- qSig(query=qmat, gess_method="gCMAP", refdb=db_path)
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