readSampleInfoFromGEO {limma} | R Documentation |
Read sample annotation from a GEO Series Matrix File into data.frames.
readSampleInfoFromGEO(file, remove.constant.columns = TRUE)
file |
file name or path of GEO series matrix file. |
remove.constant.columns |
logical, if |
This function parses a GEO series matrix file. Sample characteristics associated with expression channels 1 and 2 are separated into separate data.frames. The function particularly allows for the fact that not every sample characteristic will have an entry for every sample.
A list with three components:
SampleInfo |
character matrix of sample annotation. |
CharacteristicsCh1 |
character matrix of sample characteristics associated with expression channel 1. |
CharacteristicsCh2 |
character matrix of sample characteristics associated with expression channel 2. |
Each sample corresponds to one row.
Gordon Smyth
An overview of LIMMA functions for reading data is given in 03.ReadingData.
# This example downloads a series matrix file of about 33MB ## Not run: url <- "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE40nnn/GSE40115/matrix/GSE40115-GPL15931_series_matrix.txt.gz" download.file(url, "GSE40115.txt.gz") a <- readSampleInfoFromGEO("GSE40115.txt.gz") colnames(a$SampleInfo) colnames(a$CharacteristicsCh1) colnames(a$CharacteristicsCh2) ## End(Not run)