pm.getabst: Obtain the abstracts for a set PubMed list.
In annotate: Annotation for microarrays
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
Description
The data provided by PubMed is reduced to a small set. This set is
then suitable for further rendering.
Usage
1
pm.getabst(geneids, basename)
Arguments
geneids
The identifiers used to find Abstracts
basename
The base name of the annotation package to use.
Details
We rely on the annotation in the package associated with the
basename to provide PubMed identifiers for the genes described by
the gene identifiers.
With these in hand we then use the pmfetch utility to download the
PubMed abstracts in XML form. These are then translated (transformed) to a
shorter version containing a small subset of the data provided by PubMed.
This function has the side effect of creating an environment in
.GlobalEnv that contains the mapping for the requested data.
This is done for efficiency – so we don't continually read in the data
when there are many different queries to be performed.
Value
A list of lists containing objects of class pubMedAbst.
There will be one element of the list for each identifier.
Each of these elements is a list containing one abstract (of
class pubMedAbst for each PubMed identifier associated with
the gene identifier.
Author(s)
Robert Gentleman
See Also
Examples
1
2
3
library("hgu95av2.db")
hoxa9 <- "37806_at"
absts <- pm.getabst(hoxa9, "hgu95av2")
annotate documentation built on Nov. 8, 2020, 8:14 p.m.
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Description Usage Arguments Details Value Author(s) See Also Examples
Description
The data provided by PubMed is reduced to a small set. This set is then suitable for further rendering.
Usage
1 | pm.getabst(geneids, basename)
|
Arguments
geneids |
The identifiers used to find Abstracts |
basename |
The base name of the annotation package to use. |
Details
We rely on the annotation in the package associated with the
basename to provide PubMed identifiers for the genes described by
the gene identifiers.
With these in hand we then use the pmfetch utility to download the
PubMed abstracts in XML form. These are then translated (transformed) to a
shorter version containing a small subset of the data provided by PubMed.
This function has the side effect of creating an environment in
.GlobalEnv that contains the mapping for the requested data.
This is done for efficiency – so we don't continually read in the data
when there are many different queries to be performed.
Value
A list of lists containing objects of class pubMedAbst.
There will be one element of the list for each identifier.
Each of these elements is a list containing one abstract (of
class pubMedAbst for each PubMed identifier associated with
the gene identifier.
Author(s)
Robert Gentleman
See Also
Examples
1 2 3 | library("hgu95av2.db")
hoxa9 <- "37806_at"
absts <- pm.getabst(hoxa9, "hgu95av2")
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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