Trouble using crossmeta: could not find function

Question

[monkey-bars]

I am having trouble using the crossmeta package for analyzing GEO datasets. The library downloaded fine and I got through the first few steps without any issues:

library(crossmeta)

# specify where data will be downloaded
data_dir <- file.path(getwd(), "data", "LY")

# gather all GSEs
gse_names  <- c("GSE9601", "GSE15069", "GSE50841", "GSE34817", "GSE29689")

# gather Illumina GSEs (see 'Checking Raw Illumina Data')
illum_names <- c("GSE50841", "GSE34817", "GSE29689")

# download raw data
# get_raw(gse_names, data_dir)

But once I tried the next command:

# this is why we gathered Illumina GSEs
 open_raw_illum(illum_names, data_dir)

I got this error:

Error in open_raw_illum(illum_names, data_dir) : 
  could not find function "open_raw_illum"

Can anyone help me figure out how to get it to recognize the command? Here is the link to the guide I am trying to follow: https://bioconductor.org/packages/devel/bioc/vignettes/crossmeta/inst/doc/crossmeta-vignette.html

[Ram]

Did the library load successfully? The error message says it did not.

open_raw_illum is not part of the crossmeta package - it is mentioned in the vignette and in a function header, but there is no such function in the source code. I wonder where the developer is getting it from.

I think you should post this on bioC support and/or the author's github repo.

[zx8754]

Related post at StackOverflow lists possible causes for this error:

• Error: could not find function … in R

Answer 1

[monkey-bars]

Okay, thank you. I did look through all of the commands for the package, and that one is not listed, so I have no idea where it came from. I'll reach out to the author and see if I can get any insight.

• GitHub issue 8 Code "open_raw_illum" not working