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CIBERSORT

The goal of CIBERSORT is to run the CIBERSORT flow.

Installation

You can install the released version of CIBERSORT from github with:

install.packages("devtools")
devtools::install_github("Moonerss/CIBERSORT")

Example

library(CIBERSORT)
sig_matrix <- system.file("extdata", "LM22.txt", package = "CIBERSORT")
mixture_file <- system.file("extdata", "exampleForLUAD.txt", package = "CIBERSORT")
results <- cibersort(sig_matrix, mixture_file)

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cibersort's Issues

error

Warning messages:
1: package ‘preprocessCore’ is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
2: In file.copy(savedcopy, lib, recursive = TRUE) :
problem copying D:\Software\R-4.1.2\library\00LOCK\rlang\libs\x64\rlang.dll to D:\Software\R-4.1.2\library\rlang\libs\x64\rlang.dll: Permission denied
3: In file.copy(savedcopy, lib, recursive = TRUE) :
problem copying D:\Software\R-4.1.2\library\00LOCK\glue\libs\x64\glue.dll to D:\Software\R-4.1.2\library\glue\libs\x64\glue.dll: Permission denied
4: In file.copy(savedcopy, lib, recursive = TRUE) :
problem copying D:\Software\R-4.1.2\library\00LOCK\cli\libs\x64\cli.dll to D:\Software\R-4.1.2\library\cli\libs\x64\cli.dll: Permission denied
5: In file.copy(savedcopy, lib, recursive = TRUE) :
problem copying D:\Software\R-4.1.2\library\00LOCK\magrittr\libs\x64\magrittr.dll to D:\Software\R-4.1.2\library\magrittr\libs\x64\magrittr.dll: Permission denied
6: In file.copy(savedcopy, lib, recursive = TRUE) :
problem copying D:\Software\R-4.1.2\library\00LOCK\vctrs\libs\x64\vctrs.dll to D:\Software\R-4.1.2\library\vctrs\libs\x64\vctrs.dll: Permission denied
7: In i.p(...) :
installation of package ‘C:/Users/zy/AppData/Local/Temp/RtmpKCkGse/remotes517498d752b/CIBERSORT-main’ had non-zero exit status

when I run the code "library(CIBERSORT)"

it showed the result below:

library(CIBERSORT)
Error in library(CIBERSORT) : 不存在叫‘CIBERSORT’这个名字的程辑包

Who can tell me how to use this package?

error

excuse me ,I am facing an issue when running CIBERSORT package:
when I try this:

library(CIBERSORT)

sig_matrix <- system.file("extdata", "LM22.txt", package = "CIBERSORT")

mixture_file <- system.file("extdata", "exampleForLUAD.txt", package = "CIBERSORT")

data(LM22)
LM22[1:4,1:4]#547 22
#      B cells naive B cells memory Plasma cells T cells CD8
#ABCB4     555.71345       10.74423     7.225819     4.31128
#ABCB9      15.60354       22.09479   653.392328    24.22372
#ACAP1     215.30595      321.62102    38.616872  1055.61338
#ACHE       15.11795       16.64885    22.123737    13.42829

data(mixed_expr)
mixed_expr[1:4,1:4]#[1] 20501     5
#      TCGA-05-4244-01 TCGA-05-4249-01 TCGA-05-4250-01 TCGA-05-4382-01
#A1BG          26.0302        120.1349         50.8597        145.9037
#A1CF           0.0000          0.3220          0.0000          0.0000
#A2BP1          1.7454          1.6098          0.0000          0.0000
#A2LD1        135.5022         89.0629        151.1332        112.0685

and running it:

> results <- cibersort(sig_matrix = LM22, mixture_file = mixed_expr,perm = 1000,QN = T)
Error in normalize.quantiles(Y) : 
  ERROR; return code from pthread_create() is 22

how can I do for this error?
hoping your help ......

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