Extract Raw Count Matrix from Supplementary Files.
Usage
ExtractGEOExpSupp(
acce,
timeout = 3600,
supp.idx = 1,
file.regex = NULL,
extra.cols = c("chr", "start", "end", "strand", "length", "width", "chromosome",
"seqnames", "seqname", "chrom", "chromosome_name", "seqid", "stop"),
transpose = TRUE
)Arguments
- acce
GEO accession number.
- timeout
Timeout for
download.file. Default: 3600.- supp.idx
The index of supplementary files to download. Default: 1.
- file.regex
The regex to extract correct count matrix files. Default: NULL.
- extra.cols
Extra columns to remove, e.g., "Chr", "Start", "End", "Strand", "Length" (featureCounts).
- transpose
Logical value, whether to transpose the matrix. Used when the number of rows is less than the number of columns.