​R语言阈值置信区间怎么计算

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R语言源代码

####################################Arg<-commandArgs(TRUE)###########input###############################################individual_analysis<- c(Arg[1])reprication<-c(Arg[2])filter_value<-c(Arg[3])population_structure<-c(Arg[4]) #RIL or F2depth_analysis<-c(1:300)###########input##########################################################genotype#############################genotype<-function(){count<-0if (population_structure=="RIL"){x<-runif(1) if (x<=0.5){count<-1}else{count<-0}}else{for(i in 1:2){x<-runif(1) if (x<=0.5){number<-0.5}else{number<-0}if(number == 0.5){count<- count+0.5}}}return(count)}#######################################################################caluclate of genotype ratio#########################individuals_genotype<-function(number_of_total_individuals){ratio_of_genotype<-c()for(i in 1:number_of_total_individuals){ratio_of_genotype<-c(ratio_of_genotype,genotype())}return(mean(ratio_of_genotype))}#######################################################################SNP_index_caluclation#########################snp_index<-function(read_depth,ratio_of_genotype_in_the_population_in_A){x1<-rbinom(1,read_depth,ratio_of_genotype_in_the_population_in_A)return(x1/read_depth)}################################################################################################for (key_individual in individual_analysis){   individual_number<-key_individual        depth_data<-c()    p_l_data_95<-c()    p_h_data_95<-c()    p_l_data_99<-c()    p_h_data_99<-c()    for (key_depth in depth_analysis){        depth_data<-c(depth_data,key_depth)        depth<-key_depth            data_of_delta_snp_index<-c()                for(i in 1:reprication){            ##########gene_frequency######################ratio_of_genotype_in_the_population_in_A<-individuals_genotype(key_individual)Snp_index_of_A<-snp_index(key_depth,ratio_of_genotype_in_the_population_in_A)ratio_of_genotype_in_the_population_in_B<-individuals_genotype(key_individual)Snp_index_of_B<-snp_index(key_depth,ratio_of_genotype_in_the_population_in_B)if(Snp_index_of_A >= filter_value | Snp_index_of_B >=filter_value){delta_snp_index<-Snp_index_of_A-Snp_index_of_Bdata_of_delta_snp_index<-c(data_of_delta_snp_index,delta_snp_index)}##########gene_frequency######################        }                order_data_of_delta_snp_index<-sort(data_of_delta_snp_index)        length_data_of_delta_snp_index<-length(data_of_delta_snp_index)        ##########snp_index_probabirity_0.05######################               snp_cutoff_low_0.025<-order_data_of_delta_snp_index[floor(0.025*length_data_of_delta_snp_index)]snp_cutoff_up_0.975<-order_data_of_delta_snp_index[ceiling(0.975*length_data_of_delta_snp_index)]p_l_data_95<-c(p_l_data_95,snp_cutoff_low_0.025)        p_h_data_95<-c(p_h_data_95,snp_cutoff_up_0.975)           ##########snp_index_probabirity_0.05######################                ##########snp_index_probabirity_0.01######################         if (floor(0.005*length_data_of_delta_snp_index)>0){        snp_cutoff_low_0.005<-order_data_of_delta_snp_index[floor(0.005*length_data_of_delta_snp_index)]        }else{        snp_cutoff_low_0.005<-order_data_of_delta_snp_index[1]        }                      if (ceiling(0.995*length_data_of_delta_snp_index)
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