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Genometric / MSPC

Using combined evidence from replicates to evaluate ChIP-seq peaks
https://genometric.github.io/MSPC/
GNU General Public License v3.0
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C argument does not accept percentage #191

Closed sufyazi closed 1 year ago

sufyazi commented 1 year ago

While running MSPC, I wanted to specify 50% for the c argument on rmspc (from Bioconductor), as described here. However, the program threw me a warning Warning: Invalid C=50, it is set to C=5. and proceeded to use 5 as the parameter value for the run.

Context: I had 5 biological replicated input peak files. The code I use to run rmspc specifically was as follows:

results <- mspc(input = input_paths, replicateType = "Bio", stringencyThreshold = 1e-8, weakThreshold = 1e-4, gamma = 1e-8, keep = TRUE, multipleIntersections = "Lowest", c = 50, alpha = 0.05, inputParserConfiguration = parser_json, outputPath = output_path)

Is it because I did not use % symbol? I removed it because my VSCode linter disliked that symbol there so I thought it is going to error out if I run the command.

Tangential question: Considering the robustness of the MSPC analysis under the hood, do you have any recommendation for the value of C? Would setting it to the number of input samples be too stringent/remove potentially true peaks? The default setting is 1; is there any justification for this design decision that I am not seeing?

VJalili commented 1 year ago

You need to use % if you want to specify the percentage of input as the value of c. Please see this example.

Tangential question: Considering the robustness of the MSPC analysis under the hood, do you have any recommendation for the value of C? Would setting it to the number of input samples be too stringent/remove potentially true peaks? The default setting is 1; is there any justification for this design decision that I am not seeing?

Does this help?

sufyazi commented 1 year ago

Hi Vahid, the link to answer my second question helped a lot! It makes so much sense and does tally with how I understood the design based from what I have read in your paper and documentation. Thank you.

I reran the command with the % symbol and it worked. Appreciate the help! Feel free to close this issue.

VJalili commented 1 year ago

Awesome! glad those were useful @sufyazi!

I am closing this issue, and please feel free to re-open it if needed.