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Error in UseMethod("isSymmetric") : no applicable method for 'isSymmetric' applied to an object of class "c('double', 'numeric')" #5

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changostraw opened this issue Jul 3, 2024 · 0 comments

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@changostraw
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changostraw commented Jul 3, 2024

Hi,
Thanks for the package. I have applied it a few times successfully, but now I am getting this error.

r/4.3.1
library(FastCAR) library(Matrix) library(Seurat) library(qlcMatrix) library(pheatmap) library(ggplot2) library(gridExtra) library(stringr)

cellMatrix = Read10X("/project/rrg-gturecki/Sarah/Multiplexing_Test/MT_test1/MT_multiseq_INS_PoolE_count_newref/outs/filtered_feature_bc_matrix/")
fullMatrix = `Read10X("/project/rrg-gturecki/Sarah/Multiplexing_Test/MT_test1/MT_multiseq_INS_PoolE_count_newref/outs/raw_feature_bc_matrix/")

ambProfile = describe.ambient.RNA.sequence(fullMatrix = fullMatrix, 
                                           start = 50, 
                                           stop = 500, 
                                           by = 50, 
                                           contaminationChanceCutoff = 0.01)

pdf(file = "/project/rrg-gturecki/Sarah/Multiplexing_Test/MT_test1/AmbientRNA/MT_INS_PoolE_newref/FastCAR/ambient_profile.pdf", width = 4, height = 4)
plot.ambient.profile(ambProfile)
dev.off()

correctionEffectProfile = describe.correction.effect(fullMatrix, cellMatrix, 50, 500, 50, 0.1)
pdf(file = "/project/rrg-gturecki/Sarah/Multiplexing_Test/MT_test1/AmbientRNA/MT_INS_PoolE_newref/FastCAR/correct_effect_heatmap.pdf", width = 4, height = 4)
plot.correction.effect.chance(correctionEffectProfile)
dev.off()

emptyDropletCutoff = recommend.empty.cutoff(ambProfile)
emptyDropletCutoff

emptyDropletCutoff        = 350 
contaminationChanceCutoff = 0.05

ambientProfile = determine.background.to.remove(fullMatrix, emptyDropletCutoff, contaminationChanceCutoff)
cellMatrix = remove.background(cellMatrix, ambientProfile)

Error in UseMethod("isSymmetric") :
no applicable method for 'isSymmetric' applied to an object of class "c('double', 'numeric')"

Thanks!

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