search for: mir

...ldn't work out how to get the output I want. I have also considered rearranging this data into a list (by gene) and then counting the length of each gene element. However I thought that there might be a more elegant solution. Tanaka Mitchell Wang Hunter Chen Chim miR-191* let-7e let-7b miR-126 let-7a let-7g miR-198 let-7f let-7c miR-146a let-7b let-7i miR-22 let-7g miR-1224 miR-16 let-7d miR-130b miR-223 let-7i miR-124 miR-191 let-7f miR-133a miR-296 let7fG15A miR-125a-3pmi...

Through converting a miRNAs file from FASTA to character format I get a vector which looks like the following: > nml [1] "hsa-let-7a MIMAT0000062 Homo sapiens let-7a" [2] "hsa-let-7b MIMAT0000063 Homo sapiens let-7b" [3] "hsa-let-7c MIMAT0000064 Homo sapiens let-7...

Hello list. I have a vector of values: eg > head(diff_mirs_list) [1] "hsa-miR-26b" "hsa-miR-26b" "hsa-miR-23a" "hsa-miR-27b" "hsa-miR-29a" [6] "hsa-miR-29b" and I would like to conditionally replace each value in this vector with a number defined in a dataframe: > fc ???????????? Probe ave.f...

Hi, There is a question that I am confused. I have a set of data like this: hsa-miR-205--GATA3 0.797882767 1.08E-13 hsa-miR-205--ITGB4 0.750217593 1.85E-11 hsa-miR-187--PGF 0.797604155 3.24E-11 hsa-miR-205--SERPINB5 0.744124886 3.28E-11 hsa-miR-205--PBX1 0.734487224 7.89E-11 hsa-miR-205--MCC 0.72499934 1.80E-10 hsa-miR-205--WNT5B 0.717705259 3.33E-10 hsa-miR-200c--PK...

Dear list, I am sorry about this simple question, but somehow I can not figure out how to solve my problem, may be you could help? I have a vector mir3: > length(mir3) [1] 220671 >head(mir3) rno-miR-30c rno-miR-30c rno-miR-30d rno-miR-30e "ENSRNOT00000049288" "ENSRNOT00000049288" "ENSRNOT00000049288" "ENSRNOT00000049288" rno-miR-145...

hi everybody, i try to extract a part of name to a date : like : "VGT1_VGT2_CONTR_B020030401.H0V0.MIR" to "20030401" but the beginning of the files changes i have a list of files: [,1] [1,] "VGT1_CONTR_B020020301.H0V0.MIR" [2,] "VGT1_VGT2_CONTR_B020020611.H0V0.MIR" [3,] "VGT1_VGT2_CONT...

...;,"a","b","b","c","c","d","d","e","e","f","f")) }/ *The function is supposed plot a row from the following input-table:* / X1h X4h X9h X15h X18h X21h hsa-miR-99b* 173 64 66 56 65 65 hsa-miR-99b 549 697 1070 1051 1777 2201 hsa-miR-99a* 3 1 3 0 3 2 hsa-miR-99a 5 4 14 16 33 37 hsa-miR-98 3475 4177 4075 4513 4631 5940 hsa-miR...

Hello, I am trying to isolate an assertion failure in if-converter (on PPC) and I generated a textual debuglog with: ``` LLVM_ARGS=-print-before-all -print-module-scope -filter-print-funcs=japi1__require_7687 ``` and after splicing out the the MIR before the if-converter pass I would like to run `llc -march=ppc64le -run-pass=if-converter input.mir` so that I can start minimising the MIR. This steps fails for me with a: ``` error: YAML:188:20: Unrecognized character while tokenizing. Function Live Ins: %x4 ^ error: YAML:1...

...https://github.com/microsoft/llvm-mctoll On Mon, Nov 25, 2019 at 1:19 PM Nicolai Hähnle via llvm-dev < llvm-dev at lists.llvm.org> wrote: > On Thu, Nov 21, 2019 at 3:37 AM Lele Ma via llvm-dev > <llvm-dev at lists.llvm.org> wrote: > > My goal is to write LLVM Machine IR (MIR) passes to analyze the assembly > source code. But it seems I need to find a way to translate the handwritten > assembly code into MIR format first. > > > > Is there any materials, or any modules in LLVM source code, that can > help to translate assembly code into LLVM MIR for...

Hello Valentin, To generate a mir test case i think the process is to first create an IR file by passing '-S -emit-llvm' to clang, then you can feed that file into llc and use stop-before to get the mir just before the if-converter pass, eg: `llc -stop-before=if-converter -simplify-mir -o test.mir test.ll`. Also there is...

Valentin, in terms of limitations as Sean pointed out, an important one is that .mir doesn't have MachineFunctionInfo which may result in failure on accesses to global variables due to use of register X2. The verifier considers it an undefined register. Also, it's probably easier to reduce test cases using bugpoint starting from an IR test case. With the code you provided,...

Hi all, The CodeGen library is a big bag of interdependent bits. This caused a circular dependency in the MIR serialization commit (r237954), which got reverted in r238007. I propose separating the machine IR out of CodeGen and into its own MIR library, living at lib/MIR. This touches every target but it's mostly a mechanical change that renames the header files, although a couple of pre-rename commit...

...l, A self-follow up and rephrase of my previous question with updated subject: What I want to do is to analyze hand-written assembly code with 'full details' where semantics of each instruction can be known in LLVM passes. Many of such instructions have no corresponding counterparts in IR/MIR forms, such as 'syscall' 'iret', etc. At MC level, such assembly code can be translated to MCInst easily since this level is closest to the assembly code. Therefore, I am thinking to write a pass at MC level instead of IR/MIR. However, when I am searching to learn the MC level pass...

Hi, My name is Puyan and I've been exploring ways to improve the state of instruction level diffing using llvm and MIR. Below is a proposal for a new llvm tool meant to address issues encountered when diffing at the machine level. I'm eager to hear the community's feedback. Thanks PL mir-canon: A new tool for canonicalizing MIR for cleaner diffing. Problem Statement and Context: Diff-tools are regu...

Thank you both! I was running into the issue that bugpoint was reducing my test-case into other failures and I hadn't managed yet to find the right point in the Julia pass pipeline to insert the module to reproduce the issue reliably from llc and that's why I started looking at using the MIR. I will go back at looking at the pass pipeline and the IR and get a reproducer that way! Thanks, Valentin On Tue, 20 Mar 2018 at 07:51 Nemanja Ivanovic <nemanja.i.ibm at gmail.com> wrote: > Valentin, > in terms of limitations as Sean pointed out, an important one is that .mir >...

...LLVM :: CodeGen/AMDGPU/promote-alloca-bitcast-function.ll LLVM :: CodeGen/ARM/2012-09-25-InlineAsmScalarToVectorConv2.ll LLVM :: CodeGen/BPF/many_args1.ll LLVM :: CodeGen/BPF/many_args2.ll LLVM :: CodeGen/BPF/struct_ret1.ll LLVM :: CodeGen/BPF/struct_ret2.ll LLVM :: CodeGen/MIR/Generic/invalid-jump-table-kind.mir LLVM :: CodeGen/MIR/Generic/llvm-ir-error-reported.mir LLVM :: CodeGen/MIR/Generic/machine-function-missing-function.mir LLVM :: CodeGen/MIR/Generic/machine-function-missing-name.mir LLVM :: CodeGen/MIR/Generic/machine-function-redefinition-error....

Hello List I'm moving this over from the bioC list as, although the problem I'm working on is biological, the current bottle neck is my poor understanding of R. I wonder if someone would help me with the following function. cumulMetric <- function(deMirPresGenes, deMirs){ ??? #need to match position of each miR in deMirPresGenes with its FC to form a vector of FC in correct order ? ? fc <- deMirs ? ? fcVector <- as.numeric(with (fc, FC[match(deMirPresGenes[,4], Probe)] ) ) ? ? #multiply fc by context score for each interaction ? ? metric &l...

Dear LLVM developers, My goal is to write LLVM Machine IR (MIR) passes to analyze the assembly source code. But it seems I need to find a way to translate the handwritten assembly code into MIR format first. Is there any materials, or any modules in LLVM source code, that can help to translate assembly code into LLVM MIR for analysis? Or is there any easier...

...coming days. > > PL > > On Tue, Aug 15, 2017 at 12:06 PM Puyan Lotfi <puyan.lotfi.llvm at gmail.com> > wrote: > >> Hi, >> >> >> My name is Puyan and I've been exploring ways to improve the state of >> instruction level diffing using llvm and MIR. Below is a proposal for a new >> llvm tool meant to address issues encountered when diffing at the machine >> level. I'm eager to hear the community's feedback. >> >> >> Thanks >> >> >> PL >> >> >> mir-canon: A new tool for...

I have the following list of strings: name <- c("hsa-miR-555p","hsa-miR-519b-3p","hsa-let-7a") What I want to do is for each of the above strings replace the text after second delimiter with "zzz". Yielding: hsa-miR-zzz hsa-miR-zzz hsa-let-zzz What's the way to do it? [[alternative HTML version deleted]]