dot-appendGSEColumns: Append information from GSE columns to a data frame

In ss-lab-cancerunit/SpiderSeqR: A Tool for Integration of Big Bio Data

Description

Performs search for GSEs in the gse table and fetches columns of interest, which get appended to the existing data frame. In case a sample belongs to multiple GSEs, the information appears in the same field separated with a special character.

Usage

.appendGSEColumns(df, gse_columns)

Arguments

df	Data frame with series_id column containing GSEs; gsm column is also required for join purposes
gse_columns	Character vector with names of GSE columns to be appended

Details

NOTE: pubmed_id column (in gse table from the database generated by GEOmetadb) appears to only contain approximately 20 from the online version of GEO (the rest has missing pubmed_ids)

Value

Data frame with appended gse columns (they will be named with a prepended 'GSE_')

Examples

# .appendGSEColumns(df, "pubmed_id") # Append only pubmed_id column
# .appendGSEColumns(df, "*") # Append all available columns from gse

ss-lab-cancerunit/SpiderSeqR documentation built on Nov. 2, 2020, 12:18 a.m.