The rcscs from askerdb

rcscs's Introduction

Install

Install with:

devtools::install_github("askerdb/rCSCS")

Example

Example data with fecal samples of Crohns diseased children (CD) and Healthy children (HC), run in both positive and negative ionisation mode (MassIVE ID: MSV000081120)

(requires the packages rCSCS, ape, and ggplot2)

#Download the GNPS job
cicra <- rCSCS::prepare_GNPS("b0524246804a4b50a8a4ec6244a8be2e", "cicra_example") 
#Run CSCS on the relevant samples (The ones not labelled full scan or standard)
cicra_cscs <- rCSCS::cscs(cicra$features[-grep("FS|Standard", colnames(cicra$features))], cicra$css)
#Run PCoA
cicra_pcoa <- ape::pcoa(cicra_cscs)
#Extract the disease status
cicra_meta = unlist(lapply(strsplit(rownames(cicra_pcoa$vectors), "_" ), function(x) x[[1]]))
#Plot the data
ggplot2::ggplot(data.frame(cicra_pcoa$vectors[,1:2], Meta = cicra_meta, Name = row.names(cicra_pcoa$vectors)) ,
               ggplot2::aes(x = Axis.1, y = Axis.2, color = Meta)) + ggplot2::geom_point()  +
  ggplot2::geom_label(ggplot2::aes(label = Name))

rcscs's People

Contributors

Stargazers

Watchers

rcscs's Issues

Install problem from devtools

Installation via devtools fails with the following error

Error: (converted from warning) Setting LC_CTYPE failed, using "C" Execution haltedError: Failed to install 'rCSCS' from GitHub

MZMine workflow tutorial

Implement an extra check in cscs() to make sure the rownames of css and features matches.

Error in preparation of GNPS files

Hello,

Looking forward to trying this out but ran into some issues getting my data into it:

Is this available for GNPS jobs created using MZmine? These do not have a bucket table to download and result in an error.
I tried it with a GNPS job (ID =9144d1b70a7249809f94ef85d73ee5bb), and got the following error:

Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 1 did not have 8 elements

I think that the edge file has an extra column in it that does not appear in the tutorial, "EdgeAnnotation".

Can I manually select the necessary files? In general this would be useful (for example to edit in Cytoscape first).

Thank you!

Best,
Rachel

Recommend Projects