scDaPars

[ghost]

scDaPars.res = scDaPars(raw_PDUI_file = "/DaPars2_Test_data_result_temp.chr3.txt",out_dir = "/scDaPars_result",filter_gene_thre = 0.2,filter_cell_thre = 0.1) show error :

Error in RANN::nn2(t(mat_pcs), k = 30) : Cannot find more nearest neighbours than there are points

[YiPeng-Gao]

scDaPars.res = scDaPars(raw_PDUI_file = "/DaPars2_Test_data_result_temp.chr3.txt",out_dir = "/scDaPars_result",filter_gene_thre = 0.2,filter_cell_thre = 0.1) show error :

Error in RANN::nn2(t(mat_pcs), k = 30) : Cannot find more nearest neighbours than there are points

Can you share the size of your dataset?

[ghost]

Run DaPars2, Output format:

/scDaPars/Example/Dapars_hESC_combined_all_chromosome.txt comes out with a column of numbers. What should I do with the data after Dapars2 runs? Dapars_hESC_combined_all_chromosome.txt What information is the number in the first column?

The reason for the error when running scDapars software is that the results of DaPars2 software running are missing the first column, so scDapars cannot be run directly.

best

[learner-bioinformation]

Hi, I want to ask whether the output result of DaPars2 can be directly used as the input of scDaPars. When I input directly, the following error appears. How can I solve the following error?

[YiPeng-Gao]

Run DaPars2, Output format:

/scDaPars/Example/Dapars_hESC_combined_all_chromosome.txt comes out with a column of numbers. What should I do with the data after Dapars2 runs? Dapars_hESC_combined_all_chromosome.txt What information is the number in the first column?

The reason for the error when running scDapars software is that the results of DaPars2 software running are missing the first column, so scDapars cannot be run directly.

best

scDaPars runs directly using DaPars results. The first column are put in by mistake. I will update the github example file. You can run the file without the first column.

[ghost]

Number of samples: 7 Data size: 428K， Thank you for updating the file as soon as possible Use DaPars result files to directly analyze scDaPars, show error :

[ghost]

Number of samples: 7 Data size: 428K， Use DaPars result files to directly analyze scDaPars, show error :

[YiPeng-Gao]

Number of samples: 7 Data size: 428K， Use DaPars result files to directly analyze scDaPars, show error :

The problem here is you have too few samples. The RANN:nn2() function has a parameter k = 30. Therefore, it will give this error if the number of samples is fewer than 30 (which does not make sense for single-cell studies). Normally, in single-cell studies, you will have at least hundreds of cells.

[ghost]

Number of samples: 35 Data size: 1.7M show error :Error in 1:npc : argument of length 0

[YiPeng-Gao]

Number of samples: 35 Data size: 1.7M show error :Error in 1:npc : argument of length 0

The code and example file has been updated and the code is working smoothly right now. I cannot help you debug when I don't have your data. You can use the R scripts provided in GitHub to run code line by line to figure out the reason for this error. It seems your error happens when scDaPars selects PCs (npc) that explain >40% of the total variance for clustering. You can start from there.

[ghost]

Hello, can I add your contact information? Emails have been sent to your mailbox before, beginning with 181

[YiPeng-Gao]

Hello, can I add your contact information? Emails have been sent to your mailbox before, beginning with 181

You can email me at yipengg@bcm.edu