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License: MIT License
Left Truncated Mixture Gaussian Single Cell Analysis Model
License: MIT License
my code is :
library(LTMGSCA)
library(Matrix)
library(dplyr)
library(ggplot2)
library(ggpubr)
library(Rtsne)
library(RColorBrewer)
library(KRLS)
library(RSpectra)
library(SwarmSVM)
library(reshape2)
### Read and preprocess 10X files
PBMC<-Read10X("GRCh38")
PBMC_meta<-Data_Meta(PBMC)
my error is:
Error in colSums(MAT > 0) :
'x' must be an array of at least two dimensions
*I use the following code : *
library(LTMGSCA)
library(Matrix)
library(dplyr)
library(ggplot2)
library(ggpubr)
library(Rtsne)
library(RColorBrewer)
library(KRLS)
library(RSpectra)
library(SwarmSVM)
library(reshape2)
PBMC<-Read10X("hg19")
PBMC<-as.matrix(PBMC)
PBMC_meta<-Data_Meta(PBMC)
Plot_Meta(PBMC_meta)
#ggsave("test_meta.png",width=4,height=4,dpi=300)
PBMC<-Data_subset(PBMC,PBMC_meta,nFeature.lower = 200,nFeature.upper = 2000,Counts.upper = 5000,Percent.mt.upper = 0.1)
str(PBMC_meta)
#List of 3
# $ nFeature : Named num [1:2700] 781 1352 1131 960 522 ...
# ..- attr(*, "names")= chr [1:2700] "AAACATACAACCAC" "AAACATTGAGCTAC" "AAACATTGATCAGC" "AAACCGTGCTTCCG" ...
# $ Counts : Named num [1:2700] 2421 4903 3149 2639 981 ...
# ..- attr(*, "names")= chr [1:2700] "AAACATACAACCAC" "AAACATTGAGCTAC" "AAACATTGATCAGC" "AAACCGTGCTTCCG" ...
# $ Percent.mt: Named num [1:2700] 0.03015 0.03794 0.00889 0.01743 0.01223 ...
# ..- attr(*, "names")= chr [1:2700] "AAACATACAACCAC" "AAACATTGAGCTAC" "AAACATTGATCAGC" "AAACCGTGCTTCCG" ...
PBMC<-PBMC[rowSums(PBMC>0)>0.01*ncol(PBMC),]
PBMC<-NormalizeCount(PBMC)
Zcut_G<-log(Global_Zcut(PBMC))
head(Zcut_G)
#[1] 0
Gene<-"CCL5"
VEC<-PBMC[Gene,]
VEC_LTMG<-LTMG(VEC,Zcut_G,k=5)
plot_gene(VEC = VEC,Data_LTMG = VEC_LTMG,Zcut = Zcut_G)
Then , I got Zcut_G=0 , Then I got Zcut_G as 0. Is this correct? Also, there are three peaks in my plot_gene result ?
Hi! Could you please add man folder or annotations about the meaning of parameters and outputs in each function (e.g. I'm a little confused about the meaning of k here in LTMG function)? Thanks!
Line 427 in d3aa7e6
This variable does not seem to be defined. If there is no global variable Gene
, you will get an error.
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