Description Usage Arguments Details Value Author(s) See Also Examples
These function allow to create Report objects from data.frames (one Report object per line) or to export the contents of a Report object as a (single row) data.frame.
1 2 3 4 | data.frame2report( x, colname.pmid="references_pmid", colname.support="support_type", colname.experiments="experiments", split="//", do.unique=TRUE )
report2data.frame( x, colname.pmid="references_pmid",
colname.support="support_type", colname.experiments="experiments",
split="//", stringsAsFactors=FALSE, row.names=NULL )
|
x |
the data.frame or Report object. |
colname.pmid |
the column name in the data.frame providing the pubmed identifiers of the publication. |
colname.support |
the column name in the data.frame that provides the support type information from the miRTarBase. |
colname.experiments |
the column name in the data.frame containing the types of experiments that have been performed. |
split |
character that allow to split experiments in the experiments column. By default all experiments in a publication that provide evidence for the MTI are separated by a “//”. |
do.unique |
by default, the function returns a unique list of Report objects, i.e. if the submitted data.frame contained several rows with the same entries for pmid, support and evidence, it will return only one Report object for these. |
stringsAsFactors |
whether character strings should be automatically converted to factors. |
row.names |
would allow to set the row.names of the data.frame. |
This are helper functions that allow to transform data.frames into objects and vice versa.
A data.frame or a list of Report objects.
Johannes Rainer
data.frame2mti
, mti2data.frame
, Report
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ## get all miRNA target gene interactions (MTI) for BCL2L11 using a SQL
## query.
## Note, that we get the same MTI in multiple rows, if this MTI has been
## described in more than one publication:
con <- getMtiCon()
Res <- dbGetQuery( con, "select * from mirtarbase where target_gene='BCL2L11'" )
## the same MTI, but more than one publication.
Res[ Res$mirtarbase_id=="MIRT001206", c( "mirna", "target_gene", "references_pmid" ) ]
## create a list of Report objects.
Reps <- data.frame2report( Res )
## convert it again to a data.frame
DF <- do.call( "rbind", lapply( Reps, report2data.frame ) )
nrow( DF )
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