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I am running into this error with the mxm_ function, even though ewastools in installed and loaded, and I have already run some functions (call_genotypes, snp_outliers, ...) in the same script, but I can't run mxm_. I've tried deleting and re-downloading and installing ewastools, and have played with the order of package loading, but no success. Any clues appreciated! Thanks

Hello, when I am using ewastools::detectionP(raw = meth), I found some values in my detection p matrix res_list$detP are NAs, and these NAs are not consistent between samples. Are these probes with NA out-of-band probes, or they are probes that failed to detect for some samples? Thank you so much!

Unfotunately, I can't install this package with R 3.6.1 on Ubuntu 19.04 because illuminaio is not available:

> devtools::install_github("hhhh5/ewastools")
Downloading GitHub repo hhhh5/ewastools@master
Skipping 1 packages not available: illuminaio
Installing 3 packages: illuminaio, mblm, igraph
Installing packages into ‘/home/tim/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
Error: Failed to install 'ewastools' from GitHub:
  (converted from warning) package ‘illuminaio’ is not available (for R version 3.6.1)

Would ewastools support mouse methylation array ? Thanks!

In reference to the Bisulfite Conversion I metrics, I noticed this method of string matching: name %like% "I-C[12]". It looks like this filter won't match the C1 or U1 probe types because their names are, inexplicably, of the format "I C1" and "I U1" (lacking the dash). If true, only C2 and U2 probes are being returned.

Hi,
there seems to be an error with the check_sex function.

chrX = manifest[chr == "X", index]
chrY = manifest[chr == "Y", index]
create empty objects because in the manifest, column chr contains "chrX" and "chrY" instead of "X" and "Y".

I deleted the "chr" in the manifest$chr column as a workaround

Hi, I see from other posts that dropping probes from the raw object will affect the probe indices, but I'm working with non-human primates and have only a susbset of valid probes on the array. What would be the correct way to address this issue, so that I can run the control metrics only using my validated probes? Thanks for any suggestions!

Hi there,

I am trying to run this code from the vignette:

beta = meth %>% detectionP %>% mask(0.01) %>% correct_dye_bias %>% dont_normalize

but I am getting this error:

Error in mask(., 0.01) : unused argument (0.01)

Any ideas why this error might be popping up now? I've used this code as recently as a few weeks ago and not had problems.

Thanks for your help!

Edward

Dear Jonathan,

I found it a bit hard to filter probes using the list output from read_idats() function, because the probe index tend to be different between matrices, is there a good way recommended to filter unwanted probes? Thank you so much!

Best regards
Qianhui