parse_gsm_list: Parse key-value pairs in GEO series soft file
In Yunuuuu/rgeo: R interface for GEO database
parse_gsm_list R Documentation
Parse key-value pairs in GEO series soft file
Description
Lots of GSEs now use "characteristics_ch*" meta header data for key-value
pairs of annotation. If that is the case, this simply cleans the GSM
GEOSoft @meta slot up and transforms the keys to column names and the
values to column values.
Usage
parse_gsm_list(gsm_list)
Arguments
gsm_list
A list of GEOSoft, especially for @gsm slot in a GEOSeries
object.
Value
a data.frame whose rows are samples and columns are the sample infos
Examples
gse201530_soft <- rgeo::get_geo(
"GSE201530",
dest_dir = tempdir(),
gse_matrix = FALSE
)
rgeo::parse_gsm_list(rgeo::gsm(gse201530_soft))
Yunuuuu/rgeo documentation built on Dec. 23, 2024, 10:01 p.m.
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| parse_gsm_list | R Documentation |
Parse key-value pairs in GEO series soft file
Description
Lots of GSEs now use "characteristics_ch*" meta header data for key-value
pairs of annotation. If that is the case, this simply cleans the GSM
GEOSoft @meta slot up and transforms the keys to column names and the
values to column values.
Usage
parse_gsm_list(gsm_list)
Arguments
gsm_list |
A list of GEOSoft, especially for @gsm slot in a |
Value
a data.frame whose rows are samples and columns are the sample infos
Examples
gse201530_soft <- rgeo::get_geo(
"GSE201530",
dest_dir = tempdir(),
gse_matrix = FALSE
)
rgeo::parse_gsm_list(rgeo::gsm(gse201530_soft))
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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