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MillerLab-CPHG / Human_athero_scRNA_meta

This repo contains scripts used for the Human Atherosclerosis scRNA-seq meta-analysis project.
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running problem about seuratSCTprocess #3

Open Gracebio opened 1 month ago

Gracebio commented 1 month ago

hi,

I'm really interested in scRNAutils and want to apply this brilliant procession to project. Recently I researched this package and related paper before repeat this integration part. Today I installed the newest scRNAutils version(dev) and to run as the following code step by step used one sample GSM4705589_RPE004_matrix.txt firstly. raw_counts_processing/process_pan_human_carotid_samples_SCTransform.R When it came to this step,

##################################
# STEP 1: Pre-processing (Create Seurat obj containing doublets)
# Dims of seurat object: 15179 genes x 2614 cells
rpe004_seurat_sct = CreateSeuratObject(counts = rpe004_sparse_mtx, 
                                      project = "pan_rpe004_carotid", 
                                      min.cells = 10, 
                                      min.features = 200)

I changed names of function and parameter according the new version, like this:

> rpe004_seurat_sct = seuratSCTprocess(rpe004_seurat_sct, libraryID = "pan_rpe004", studyID = "pan_et_al", tissueSource = "Carotid", diseaseStatus = "Atherosclerotic_plaque", seuratFilter = TRUE, age = 83, sex = "Male") the feedback is: Setting MAD-based adaptive thresholds for cells filtering... Using 3 MADs for joint metric filtering... Error in split.default(M, B) : first argument must be a vector --   Could you please provide some suggestions? Many thanks!