diff_analysis error - Githubissues

YuLab-SMU / MicrobiotaProcessWorkshop

The workshop of microbiome datasets analysis using MicrobiotaProcess

https://yulab-smu.top/MicrobiotaProcessWorkshop/

GNU General Public License v3.0

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diff_analysis error #2

Open JAkorli opened 1 year ago

JAkorli commented 1 year ago

Hello, I used to run the command below without errors until I upgraded R version to 4.2.2. Now I get the error below when I try to run the same command on the same dataset. What could be wrong?

diff_analysis(obj= ps, classgroup = "Status",

mlfun = "lda",
filtermod = "pvalue",
firstcomfun = "kruskal_test",
firstalpha = 0.05,
strictmod = TRUE,
secondcomfun = "wilcox_test",
subclmin = 3,
subclwilc = TRUE,
secondalpha = 0.01,
lda=3)

Error in kruskal_test(k__Bacteria ~ Status, data = list(Row.names = c("MB1", : could not find function "kruskal_test"

xiangpin commented 1 year ago

The kruskal_test function is from the coin package, you might need to load it by library(coin) firstly.

PS: To explore microbiome data more efficiently, the MicrobiotaProcess package was developed using TidyFramework again, you can refer to the vignette

JAkorli commented 1 year ago

Thank you for the response. I didn't realise I was missing the 'coin' package. diff_anaysis worked as it originally did once I installed 'coin'. Thanks also for the additional information on doing microbiome analyses.