Struct bed_reader::MetadataBuilder

pub struct MetadataBuilder { /* private fields */ }

Builder for Metadata.

Implementations

impl MetadataBuilder

pub fn build(&self) -> Result<Metadata, BedErrorPlus>

Create Metadata from the builder.

See Metadata::builder()

pub fn fid<I: IntoIterator<Item = T>, T: AsRef<str>>(
    &mut self,
    fid: I
) -> &mut Self

Override the family id (fid) values found in the .fam file.

By default, if fid values are needed and haven’t already been found, they will be read from the .fam file. Providing them here avoids that file read and provides a way to give different values.

pub fn iid<I: IntoIterator<Item = T>, T: AsRef<str>>(
    &mut self,
    iid: I
) -> &mut Self

Override the individual id (iid) values found in the .fam file.

By default, if iid values are needed and haven’t already been found, they will be read from the .fam file. Providing them here avoids that file read and provides a way to give different values.

use ndarray as nd;
use bed_reader::{Bed, assert_eq_nan, sample_bed_file};
let file_name = sample_bed_file("small.bed")?;

let mut bed = Bed::builder(file_name)
   .iid(["sample1", "sample2", "sample3"])
   .build()?;
println!("{:?}", bed.iid()?); // Outputs ndarray ["sample1", "sample2", "sample3"]

pub fn father<I: IntoIterator<Item = T>, T: AsRef<str>>(
    &mut self,
    father: I
) -> &mut Self

Override the father values found in the .fam file. nd By default, if father values are needed and haven’t already been found, they will be read from the .fam file. Providing them here avoids that file read and provides a way to give different values.

pub fn mother<I: IntoIterator<Item = T>, T: AsRef<str>>(
    &mut self,
    mother: I
) -> &mut Self

Override the mother values found in the .fam file.

By default, if mother values are needed and haven’t already been found, they will be read from the .fam file. Providing them here avoids that file read and provides a way to give different values.

pub fn sex<I: IntoIterator<Item = i32>>(&mut self, sex: I) -> &mut Self

Override the sex values found in the .fam file.

By default, if sex values are needed and haven’t already been found, they will be read from the .fam file. Providing them here avoids that file read and provides a way to give different values.

pub fn pheno<I: IntoIterator<Item = T>, T: AsRef<str>>(
    &mut self,
    pheno: I
) -> &mut Self

Override the phenotype values found in the .fam file.

Note that the phenotype values in the .fam file are seldom used. By default, if phenotype values are needed and haven’t already been found, they will be read from the .fam file. Providing them here avoids that file read and provides a way to give different values.

pub fn chromosome<I: IntoIterator<Item = T>, T: AsRef<str>>(
    &mut self,
    chromosome: I
) -> &mut Self

Override the chromosome values found in the .bim file.

By default, if chromosome values are needed and haven’t already been found, they will be read from the .bim file. Providing them here avoids that file read and provides a way to give different values.

pub fn sid<I: IntoIterator<Item = T>, T: AsRef<str>>(
    &mut self,
    sid: I
) -> &mut Self

Override the SNP id (sid) values found in the .fam file.

By default, if sid values are needed and haven’t already been found, they will be read from the .bim file. Providing them here avoids that file read and provides a way to give different values.

use ndarray as nd;
use bed_reader::{Bed, assert_eq_nan, sample_bed_file};
let file_name = sample_bed_file("small.bed")?;

let mut bed = Bed::builder(file_name)
   .sid(["SNP1", "SNP2", "SNP3", "SNP4"])
   .build()?;
println!("{:?}", bed.sid()?); // Outputs ndarray ["SNP1", "SNP2", "SNP3", "SNP4"]

pub fn cm_position<I: IntoIterator<Item = f32>>(
    &mut self,
    cm_position: I
) -> &mut Self

Override the centimorgan position values found in the .bim file.

By default, if centimorgan position values are needed and haven’t already been found, they will be read from the .bim file. Providing them here avoids that file read and provides a way to give different values.

pub fn bp_position<I: IntoIterator<Item = i32>>(
    &mut self,
    bp_position: I
) -> &mut Self

Override the base-pair position values found in the .bim file.

By default, if base-pair position values are needed and haven’t already been found, they will be read from the .bim file. Providing them here avoids that file read and provides a way to give different values.

pub fn allele_1<I: IntoIterator<Item = T>, T: AsRef<str>>(
    &mut self,
    allele_1: I
) -> &mut Self

Override the allele 1 values found in the .bim file.

By default, if allele 1 values are needed and haven’t already been found, they will be read from the .bim file. Providing them here avoids that file read and provides a way to give different values.

pub fn allele_2<I: IntoIterator<Item = T>, T: AsRef<str>>(
    &mut self,
    allele_2: I
) -> &mut Self

Override the allele 2 values found in the .bim file.

By default, if allele 2 values are needed and haven’t already been found, they will be read from the .bim file. Providing them here avoids that file read and provides a way to give different values.

pub fn metadata(&mut self, metadata: &Metadata) -> &mut Self

Merge metadata from a Metadata.

Example

In the example, we create a Metadata with iid and sid arrays. Next, we use another MetadataBuilder to set an fid array and an iid array. Then, we add the first Metadata to the MetadataBuilder, overwriting iid and setting sid. Finally, we print these three arrays and chromosome. Chromosome is None.

 use ndarray as nd;
 use bed_reader::Metadata;

 let metadata1 = Metadata::builder()
     .iid(["i1", "i2", "i3"])
     .sid(["s1", "s2", "s3", "s4"])
     .build()?;
 let metadata2 = Metadata::builder()
     .fid(["f1", "f2", "f3"])
     .iid(["x1", "x2", "x3"])
     .metadata(&metadata1)
     .build()?;

 println!("{0:?}", metadata2.fid()); // Outputs optional ndarray Some(["f1", "f2", "f3"]...)
 println!("{0:?}", metadata2.iid()); // Outputs optional ndarray Some(["i1", "i2", "i3"]...)
 println!("{0:?}", metadata2.sid()); // Outputs optional ndarray Some(["s1", "s2", "s3", "s4"]...)
 println!("{0:?}", metadata2.chromosome()); // Outputs None

Trait Implementations

impl Clone for MetadataBuilder

fn clone(&self) -> MetadataBuilder

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Default for MetadataBuilder

fn default() -> Self

Returns the “default value” for a type.