convert_ids: Converts sample id's from one format to another using a data...

In chapmandu2/biotidyr: Tidy functions for MultiAssayExperiment and PharmacoGX objects

Description

Converts sample id's from one format to another using a data frame with alternate information.

Usage

convert_ids(df, id_data = NULL, from_col = "native_id",
  to_col = "unified_id", other_cols = NULL)

Arguments

df	A data frame with a column named sample_id
id_data	A data frame containing information for id conversion
from_col	Define the name of the column matching the old
to_col	Define the name of the column matching the new ids
other_cols	Other columns to include in the output

Value

a data frame

Examples

data('CCLEsmall', package='PharmacoGx')

dat1 <- gather.PharmacoSet(CCLEsmall, sample_ids=c('143B', '23132-87'), gene_ids=c('BRAF', 'EGFR'),
 data_types=c('rna', 'mutation'), gene_col=c('Symbol', 'Symbol'))

data('CancerCellLineIDs')
convert_ids(df=dat1, id_data=dplyr::filter(CancerCellLineIDs, id_type=='CCLE'),
from_col='alt_id', to_col='unified_id')
convert_ids(df=dat1, id_data=dplyr::filter(CancerCellLineIDs, id_type=='CCLE'),
from_col='alt_id', to_col='unified_id', other_cols='tissue')

chapmandu2/biotidyr documentation built on May 13, 2019, 3:29 p.m.