Closed ThomasLesser05 closed 1 year ago
Hello Thomas, I see. I've added the options of peakpicking now: you could specify the method name and SNR/window now, Please note that any missing argument will be set as default value. ` else if (preprocess$peakPick$method %in% c("adaptive","mad","simple")){
if (is.null(preprocess$peakPick$SNR)) preprocess$peakPick$SNR=6
if (is.null(preprocess$peakPick$window)) preprocess$peakPick$window=5
imdata_ed<- imdata_ed %>% peakPick(method=preprocess$peakPick$method, SNR=preprocess$peakPick$SNR, window=preprocess$peakPick$window) %>% process()
`
Thank you for your help, I will try and check! Other thing I wanted to ask, if I preprocess all data in scils software (peak picking including) - is it possible to set peakpick as Disabled?
Best wishes, Thomas
Hi, Thomas, Sure you can. Please use a ppm tolerance that fits your peak width setting in the peak-picking function.
Thank you for your help. I did not clearly understand how do you mean that - this is my code:
imaging_identification(parallel = 2, Thread = 2, datafile=datafile,Digestion_site="trypsin",threshold = 0, missedCleavages = 0:3, Fastadatabase=fastafile, output_candidatelist=T, preprocess=list(force_preprocess=T, use_preprocessRDS=TRUE, smoothSignal=list(method="Disable"), reduceBaseline=list(method="Disable"), peakPick=list(method="Disable"), peakAlign=list(tolerance=5,level="global", units="ppm"), normalize=list(method="tic")), spectra_segments_per_file=5,use_previous_candidates=F,ppm=30,FDR_cutoff = 0.01,IMS_analysis=T, Rotate_IMG=NULL, plot_cluster_image_grid=T,remove_score_outlier=F, attach_summary_cluster = F,remove_cluster_from_grid=F,plot_cluster_image_overwrite=T)
Tolerance I use for peak width is 0.1 Da. Could you please help me how to add this infomation into the code?
Thank you, Thomas
Hi, Thomas, No worries. you could consider using the preprocess$mz_bin_list to mount the reduced data properly. Here's an updated instruction: preprocess$mz_bin_list
Best, George
Hi, I am trying to use your workflow on my data using the Docker image mashuoa/hitmap:natcomms but it gets stuck during spectra preprocessing, as I work with data that are already preprocessed (I need to apply only peak picking -- S/N=2).
The code i am using:
imaging_identification(parallel = 2, Thread = 2, datafile=datafile,Digestion_site="trypsin",threshold = 0, missedCleavages = 0:3, Fastadatabase=fastafile, output_candidatelist=T, preprocess=list(force_preprocess=T, use_preprocessRDS=TRUE, smoothSignal=list(method="Disable"), reduceBaseline=list(method="Disable"), peakPick=list(SNR=1.2), peakAlign=list(method="Disable"), normalize=list(method="Disable")), spectra_segments_per_file=5,use_previous_candidates=F,ppm=30,FDR_cutoff = 0.1,IMS_analysis=T, Rotate_IMG=NULL, mzrange = c(700,3200), pixel_size_um = 20, plot_cluster_image_grid=T,remove_score_outlier=F, attach_summary_cluster = F,remove_cluster_from_grid=F,plot_cluster_image_overwrite=T)
The error I get:
Error in if (preprocess$peakPick$method == "Disable") { : argument is of length zero
Is there any option how to apply the pick picking -- Peakpick(SNR=2)? Thank you for your help!
Thomas