similar to: "invalid or not-yet-implemented 'Matrix' subsetting"

Hello list. I am hoping for some help with a relatively simple problem. I have a data frame arranged as below. I want to be able to count the occurrence of each gene (eg let-7e) by Experiment. In other words how many times does a given gene crop up in the dataframe. I tried table but couldn't work out how to get the output I want. I have also considered rearranging this data into a list (by

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.fc 1?????? hsa-let-7a?? 1.28 2?????

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--PKN2 0.721746815

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-7c" [4] "hsa-let-7d MIMAT0000065 Homo sapiens

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"

*I have the following function:* /plot_mi_time = function(mdata, miname) { mdata2 = mdata[row.names(hakat) == miname, ] print(mdata2) xcoords <- c(1,1,2,2,3,3,4,4,5,5,6,6) plot(c(xcoords), mdata2, xaxt="n", ylab="Expression", xlab="Time(h)", , main=miname) axis(1, at=xcoords,

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,]

Hi All, 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

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 a MIR language reference: https://llvm.org/docs/MIRLangRef.html

Hi all, I'd like to add a new diagnostic handler to llc. Right now, llc doesn't have one at all, and instead just exits after the first error that it encounters. This is very different from the behaviour of clang and other front ends, who try to report as many errors as possible before exiting. I think this is very important for testing LLVM's CodeGen in a more robust fashion. For

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 ?

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, I get a

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

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!

Hello, please see below my code for a heatmap. Unfortunately my column names do not completely appear. Can you please send me the appropriate code to visualise them? Many Thanks! Nils library(GMD) dat<-data.frame(EntryA=as.numeric(c(4.24,3,1.66,1.28,1.2,-1.32,-1.88)), EntryB=as.numeric(c(4.16,4.82,-1.82,-3.02,0.99,1.1,-3.31)))

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]]

I'm not sure if this helps, but here it is in case it does. I typically use bugpoint in a way as to keep the actual failure that I'm after. For example, with the test case you've pasted, I was looking for a specific assert. So I used bugpoint this way: $ cat reduceme.sh #!/bin/bash llc -filetype=obj $1 2>&1 | grep 'Cannot lower calls with arbitrary operand bundles'

In our fork of LLVM we often need to reduce a crash testcase for a specific assertion. After writing lots of "only give me this specific assertion" scripts like the above I decided to write a script that automates all this for me: <https://github.com/CTSRD-CHERI/clang/blob/master/utils/creduce_crash_testcase.py>. (It's called creduce_crash_test.py but it will actually use

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

Llvm-mctoll will raise a binary back to LLVM IR. Not exactly what you want but it might be something you can leverage. 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