User: Mohammad Alkhamis

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Posts by Mohammad Alkhamis

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Input (X) data type is not numeric if read from GRanges obj
... Hello Gunter, I noticed a minor issue in the source code (cn.mops.R) that if X is originated from a GRanges object, we end up with a matrix of integers instead of numeric/double. I guess the matrix in this case is supposed to be numeric just as if we provide X as a matrix or a vector. While it is i ...
cn.mops written 3.0 years ago by Mohammad Alkhamis0 • updated 3.0 years ago by Günter Klambauer540
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Comment: C: Attaching existing double* pointer to newly created R's SEXP struct in C/C++
... @Aaron: Thank you so much. That answers my question. @Martin: yes I am aware of that. It is just for my purpose, I need a contiguous block of memory that will later be separated to different SEXP object. It now seems that copying to SEXP object is the safest way to go. Thanks for responding :) I a ...
written 3.1 years ago by Mohammad Alkhamis0
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Attaching existing double* pointer to newly created R's SEXP struct in C/C++
... Hello everyone, I have been trying hard to figure out how to attach already-existing double pointers to SEXP vectors in C. The problem I am facing is that I have data that is processed in GPU and results are copied back to host and stored as a row-major matrix (double*). Then, I have a SEXP vector ...
R c++ written 3.1 years ago by Mohammad Alkhamis0 • updated 3.1 years ago by Aaron Lun25k
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Suggestion: type of ExpLogFoldChange (sini)
... Hello Günter, I noticed that 'ExpLogFoldChange' in the function '.cn.mopsCE' (cn.mops.R) could either be a vector or a matrix with one row as noted in the code snippet below.       if (all(x<=minReadCount)) {         [...]         ExpLogFoldChange <- rep(0,N) # this is a vector         [.. ...
cn.mops written 3.1 years ago by Mohammad Alkhamis0 • updated 3.1 years ago by Günter Klambauer540
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Answer: A: weird behaviour in R's "mean" function (precision issue)
... Never mind, I figured out the problem.. Below is the answer to the issue in case someone stumbles upon a similar issue. This is a C function that emulates the R "mean" function for real numbers. double mean_ud(double* data, unsigned int len){ long double result = 0.; unsigned in ...
written 3.2 years ago by Mohammad Alkhamis0
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parameter "refSeqName" in function "getReadCountsFromBAM"
... Hello everyone, I think that the argument "refSeqName" in the function "getReadCountsFromBAM" is a bit misleading. While looking at the source code in "getReadCountsFromBAM.R", I noticed the following code line: for (i in 1:length(refSeqName)) It turned out that I am able to use the function w ...
cn.mops written 3.3 years ago by Mohammad Alkhamis0 • updated 2.8 years ago by Günter Klambauer540
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Comment: C: why there are multiple calls to cnmops C function?
... Thank you so much Günter for your response.. that was very helpful ...
written 3.3 years ago by Mohammad Alkhamis0
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why there are multiple calls to cnmops C function?
... Hello everyone, I am trying to play with the source code for cn.mops. I inserted the following line at the beginning of the C function "cnmops", which is defined in cnmops.cpp file:  Rprintf("*** cnmops C function call ***\n");   After building the package and importing it into RStudio, I used ...
cn.mops written 3.3 years ago by Mohammad Alkhamis0 • updated 3.3 years ago by Günter Klambauer540

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