-
Notifications
You must be signed in to change notification settings - Fork 0
Open
Description
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!
Metadata
Metadata
Assignees
Labels
No labels