Plots for gene centric ncRNA regions

[samreenzafer]

Hi. I would like to also get the plots for the gene centric noncoding ncRNA regions. I see that the default (NULL) would be used for ncRNA_pos in the STAARpipeline-Tutorial/STAARpipelineSummary_Gene_Centric_Noncoding.r script, since no value is provided.

@param ncRNA_pos positions of ncRNA genes, required for generating the Manhattan plot and Q-Q plot of the results of ncRNA genes (default=NULL).

Can you please tell me what type of data structure I should provide to this argument so that I can make the script print the respective plots? I do already have the ncRNA_sig.csv file with 10 lines, and these lines are also included in the noncoding_sig.csv summary file.

[xihaoli]

Hi @samreenzafer,

Thanks for your patience. We have updated the STAARpipelineSummary package to include an R object of ncRNA_pos. Please update the STAARpipelineSummary to its latest version, and when you library(STAARpipelineSummary), ncRNA_pos will be automatically loaded in the environment and can be used for ncRNA plotting.

I have also updated the STAARpipeline-Tutorial/STAARpipelineSummary_Gene_Centric_Noncoding.r script to reflect the change as well.

Best, Xihao

[jingydz]

What does the "ncRNA_pos" refer to in the STAARpipelineSummary_Gene_Centric_Noncoding.r script?

Hello, I have utilized your most recent script (https://github.com/xihaoli/STAARpipeline-Tutorial/blob/main/STAARpipelineSummary_Gene_Centric_Noncoding.r) from the link provided, and I haven't included an additional definition for ncRNA_pos. Furthermore, I have just installed the STAARpipelineSummary package today, so it should be up to date.

Yet, I am still met with an error: 'Error: object 'ncRNA_pos' not found.' To provide more context, my Gene_Centric_Noncoding/noncoding_sig.csv file includes 107 significant genes. I attempted to set ncRNA_pos manually with the format ncRNA_pos="chr:start-end", but encountered another error: [1] "Manhattan plot", Error in UseMethod("left_join"): no applicable method for 'left_join' applied to an object of class "character"' 'Calls: Gene_Centric_Noncoding_Results_Summary -> ', after which the execution stopped.

Should I eliminate all references to ncRNA_pos, such as altering the last line of the script from alpha=alpha, ncRNA_pos=ncRNA_pos, manhattan_plot=TRUE, QQ_plot=TRUE to alpha=alpha, manhattan_plot=TRUE, QQ_plot=TRUE? Is this approach viable?

[xihaoli]

Hi @jingydz, when you library(STAARpipelineSummary), does ncRNA_pos automatically loaded to your environment?

[jingydz]

I apologize for my incorrect response earlier. The new workflow has now been successfully run without the need to define ncRNA_pos, as the new process can automatically load the necessary information. The error I experienced before was due to my own mistake of changing ncRNA_pos to ncRNApos in the code, which resulted in it not being properly recognized. I am sorry for the confusion caused.

[1] 223 [1] "Manhattan plot" [1] "ncRNA Manhattan plot" [1] "Q-Q plot" [1] "ncRNA Q-Q plot" null device 1

[xihaoli]

Hi @jingydz, thank you for confirming the ncRNA_pos can be successfully loaded and ncRNA plots can be made under the new STAARpipelineSummary package.

@samreenzafer I'll close this issue for now. Feel free to ask additional questions if you have.