Nothing
construct_sample <- function(autosomal_reads, sex_reads, name, correction_status_autosomal, correction_status_sex)
{
if(length(autosomal_reads) == 1){
rownames(autosomal_reads[[1]]) <- as.character(autosomal_chromosomes)
rownames(sex_reads[[1]]) <- XY
type = CombinedStrands
}
if(length(autosomal_reads) == 2){
rownames(autosomal_reads[[1]]) <- rownames_separated_forward_autosomal
rownames(autosomal_reads[[2]]) <- rownames_separated_reverse_autosomal
rownames(sex_reads[[1]]) <- rownames_separated_forward_sex
rownames(sex_reads[[2]]) <- rownames_separated_reverse_sex
type = SeparatedStrands
}
if ((length(correction_status_autosomal) > 1) & Uncorrected %in% correction_status_autosomal){
correction_status_autosomal <- correction_status_autosomal[-grep(pattern = Uncorrected,
x = correction_status_autosomal)]
}
if ((length(correction_status_sex) > 1) & Uncorrected %in% correction_status_sex){
correction_status_sex <- correction_status_sex[-grep(pattern = Uncorrected, x = correction_status_sex)]
}
new_sample <- list()
new_sample[[autosomal_chromosome_reads]] <- autosomal_reads
new_sample[[correction_status_autosomal_chromosomes]] <- correction_status_autosomal
new_sample[[sex_chromosome_reads]] <- sex_reads
new_sample[[correction_status_sex_chromosomes]] <- correction_status_sex
new_sample[[sample_name]] <- name
class(new_sample) <- c(NIPT_sample_class, type)
return(new_sample)
}
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