enrichshuf's People
enrichshuf's Issues
Change to foreach and doparalle
# 載入所需套件
library(foreach)
library(doParallel)
# 設定要使用的核心數量
num_cores <- 4 # 設定為您希望的核心數量
# 設定 doParallel 參數,並註冊平行處理群集
cl <- makeCluster(num_cores)
registerDoParallel(cl)
# 建立一個迴圈並使用 foreach 進行並行運算
result <- foreach(i = 1:10) %dopar% {
sqrt(i)
}
# 停止並行處理群集
stopCluster(cl)
# 查看結果
print(result)
Stop all cluster
stopImplicitCluster()
Create Anaconda environment
/mnt/nas/joseph/Anaconda3/bin/conda create -n EnrichShuf
## Optional
/mnt/nas/joseph/Anaconda3/bin/conda init bash
conda activate EnrichShuf
conda install r-essentials r-base==4.2
The following NEW packages will be INSTALLED:
_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main
_openmp_mutex pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu
_r-mutex pkgs/main/linux-64::_r-mutex-1.0.0-anacondar_1
_sysroot_linux-64~ pkgs/main/noarch::_sysroot_linux-64_curr_repodata_hack-3-haa98f57_10
binutils_impl_lin~ pkgs/main/linux-64::binutils_impl_linux-64-2.38-h2a08ee3_1
binutils_linux-64 pkgs/main/linux-64::binutils_linux-64-2.38.0-hc2dff05_0
blas pkgs/main/linux-64::blas-1.0-openblas
bwidget pkgs/main/linux-64::bwidget-1.9.11-1
bzip2 pkgs/main/linux-64::bzip2-1.0.8-h7b6447c_0
c-ares pkgs/main/linux-64::c-ares-1.18.1-h7f8727e_0
ca-certificates pkgs/main/linux-64::ca-certificates-2023.01.10-h06a4308_0
cairo pkgs/main/linux-64::cairo-1.16.0-hb05425b_3
curl pkgs/main/linux-64::curl-7.88.1-h5eee18b_0
expat pkgs/main/linux-64::expat-2.4.9-h6a678d5_0
fontconfig pkgs/main/linux-64::fontconfig-2.14.1-h52c9d5c_1
freetype pkgs/main/linux-64::freetype-2.12.1-h4a9f257_0
fribidi pkgs/main/linux-64::fribidi-1.0.10-h7b6447c_0
gcc_impl_linux-64 pkgs/main/linux-64::gcc_impl_linux-64-11.2.0-h1234567_1
gcc_linux-64 pkgs/main/linux-64::gcc_linux-64-11.2.0-h5c386dc_0
gfortran_impl_lin~ pkgs/main/linux-64::gfortran_impl_linux-64-11.2.0-h1234567_1
gfortran_linux-64 pkgs/main/linux-64::gfortran_linux-64-11.2.0-hc2dff05_0
glib pkgs/main/linux-64::glib-2.69.1-he621ea3_2
graphite2 pkgs/main/linux-64::graphite2-1.3.14-h295c915_1
gxx_impl_linux-64 pkgs/main/linux-64::gxx_impl_linux-64-11.2.0-h1234567_1
gxx_linux-64 pkgs/main/linux-64::gxx_linux-64-11.2.0-hc2dff05_0
harfbuzz pkgs/main/linux-64::harfbuzz-4.3.0-hd55b92a_0
icu pkgs/main/linux-64::icu-58.2-he6710b0_3
jpeg pkgs/main/linux-64::jpeg-9e-h5eee18b_1
kernel-headers_li~ pkgs/main/noarch::kernel-headers_linux-64-3.10.0-h57e8cba_10
krb5 pkgs/main/linux-64::krb5-1.19.4-h568e23c_0
ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.38-h1181459_1
lerc pkgs/main/linux-64::lerc-3.0-h295c915_0
libcurl pkgs/main/linux-64::libcurl-7.88.1-h91b91d3_0
libdeflate pkgs/main/linux-64::libdeflate-1.17-h5eee18b_0
libedit pkgs/main/linux-64::libedit-3.1.20221030-h5eee18b_0
libev pkgs/main/linux-64::libev-4.33-h7f8727e_1
libffi pkgs/main/linux-64::libffi-3.4.2-h6a678d5_6
libgcc-devel_linu~ pkgs/main/linux-64::libgcc-devel_linux-64-11.2.0-h1234567_1
libgcc-ng pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1
libgfortran-ng pkgs/main/linux-64::libgfortran-ng-11.2.0-h00389a5_1
libgfortran5 pkgs/main/linux-64::libgfortran5-11.2.0-h1234567_1
libgomp pkgs/main/linux-64::libgomp-11.2.0-h1234567_1
libnghttp2 pkgs/main/linux-64::libnghttp2-1.46.0-hce63b2e_0
libopenblas pkgs/main/linux-64::libopenblas-0.3.21-h043d6bf_0
libpng pkgs/main/linux-64::libpng-1.6.39-h5eee18b_0
libssh2 pkgs/main/linux-64::libssh2-1.10.0-h8f2d780_0
libstdcxx-devel_l~ pkgs/main/linux-64::libstdcxx-devel_linux-64-11.2.0-h1234567_1
libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1
libtiff pkgs/main/linux-64::libtiff-4.5.0-h6a678d5_2
libuuid pkgs/main/linux-64::libuuid-1.41.5-h5eee18b_0
libwebp-base pkgs/main/linux-64::libwebp-base-1.2.4-h5eee18b_1
libxcb pkgs/main/linux-64::libxcb-1.15-h7f8727e_0
libxml2 pkgs/main/linux-64::libxml2-2.9.14-h74e7548_0
lz4-c pkgs/main/linux-64::lz4-c-1.9.4-h6a678d5_0
make pkgs/main/linux-64::make-4.2.1-h1bed415_1
ncurses pkgs/main/linux-64::ncurses-6.4-h6a678d5_0
openssl pkgs/main/linux-64::openssl-1.1.1t-h7f8727e_0
pango pkgs/main/linux-64::pango-1.50.7-h05da053_0
pcre pkgs/main/linux-64::pcre-8.45-h295c915_0
pcre2 pkgs/main/linux-64::pcre2-10.37-he7ceb23_1
pixman pkgs/main/linux-64::pixman-0.40.0-h7f8727e_1
r-base pkgs/r/linux-64::r-base-4.2.0-h1ae530e_0
r-essentials pkgs/r/linux-64::r-essentials-0.1.0-r42h76d94ec_0
readline pkgs/main/linux-64::readline-8.2-h5eee18b_0
sysroot_linux-64 pkgs/main/noarch::sysroot_linux-64-2.17-h57e8cba_10
tk pkgs/main/linux-64::tk-8.6.12-h1ccaba5_0
tktable pkgs/main/linux-64::tktable-2.10-h14c3975_0
xz pkgs/main/linux-64::xz-5.2.10-h5eee18b_1
zlib pkgs/main/linux-64::zlib-1.2.13-h5eee18b_0
zstd pkgs/main/linux-64::zstd-1.5.2-ha4553b6_0
Speed up the Tools
To speed up the EnrichShuf, we could
- Use
GenomicRanges
insteat ofChIPseeker
.
valr delete the parameter in n_fileds in read_bed()
Build up the item with S4 objects
To rigorously define the object utilized in EnrichShuf
, we converted it into an S4 object.
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