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run.m
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run.m
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clear; clc;
tic
data_dir='data/'%'D:/AanchalMongia_phdClg/Phd/DATA_SINGLE_CELL/'
addpath(genpath('Dependencies'));
addpath(genpath('functions'));
dataname='Preimplantation'
%% Data read
if(strcmp(dataname, 'Usoskin') | strcmp(dataname,'Zeisel') )
data=csvread([data_dir 'raw_data/' dataname '_raw_data.csv'],1,1)' ;
else
sample_dir = [data_dir 'raw_data/' dataname '_dataset/hg19'];
[data, gene_names, gene_ids, cells] = read_raw_10x( strcmp(dataname,'Preimplantation') ,sample_dir);% 0 for jurkat,1 for zygote
end
%% CALL MCIMPUTE
[data_recovered,~,data_recovered_raw, gene_names]=call_mcImpute(data,'dataname',dataname);%,'gene_names',gene_names,'gene_ids', gene_ids,'pro_dir',pro_dir);
%% Save results
mkdir(['RecoveredMatrices/' dataname '_imputed']);
save(['RecoveredMatrices/' dataname '_imputed/rec.mat'],'data_recovered')
time_taken=toc