input.h File Reference

Read the a row-by-row collection of data samples from a file. More...

#include <config.h>
#include <stdlib.h>
#include <inttypes.h>
#include <jwsc/vector/vector.h>
#include <jwsc/matrix/matrix.h>
#include <jwsc/matblock/matblock.h>

Go to the source code of this file.

Enumerations
enum	Haplo_input_format { HAPLO_INPUT_TXT, HAPLO_INPUT_CSV, HAPLO_INPUT_XML }
	Types of input file format to read. More...
Functions
Error *	read_input (Matblock_u8 **ids_out, Vector_u32 **labels_out, Matrix_i32 **markers_out, const char *fname)
	Reads the IDs, haplo labels and markers from a file.
Error *	read_aux_input (Matblock_u8 **ids_out, Vector_u32 **labels_out, Matrix_i32 **markers_out, const char *fname)
	Reads the IDs, haplo labels and markers from an auxiliary file.
Error *	impute_missing_markers_from_avg (const Vector_u32 *imp_labels, Matrix_i32 *imp_markers, const Vector_u32 *src_labels, const Matrix_i32 *src_markers)
	Imputes missing marker values (zero) with their label-dependent mean value.
Error *	impute_from_parent_of_haplogroup_index (uint32_t haplo_group_index, uint32_t marker_no, uint32_t sample_no, Matrix_i32 *marker_sums, Matrix_i32 *imp_markers)
	imputes a given marker with the values from the parent haplogroup this happens when we have only one sample with a given haplogroup
Error *	impute_missing_markers_from_nn (Matrix_i32 *imp_markers, const Matrix_i32 *src_markers)
	Imputes missing marker values (zero) from nearest neighbor interpolation.

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Detailed Description

Read the a row-by-row collection of data samples from a file.

Author:

Joseph Schlecht

License:

Creative Commons BY-NC-SA 3.0

Definition in file input.h.

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Enumeration Type Documentation

enum Haplo_input_format

Types of input file format to read.

Enumerator:

HAPLO_INPUT_TXT
HAPLO_INPUT_CSV
HAPLO_INPUT_XML

Definition at line 61 of file input.h.

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Function Documentation

Error* read_input	(	Matblock_u8 **	ids_out,
		Vector_u32 **	labels_out,
		Matrix_i32 **	markers_out,
		const char *	fname
	)

Reads the IDs, haplo labels and markers from a file.

Parameters:

ids_out	Result parameter. If opts.id_cols is zero *ids_out will be NULL.
labels_out	Result parameter. If opts.labels_col is zero *labels_out will be NULL.
markers_out	Result parameter. Will always be defined, unless there was an error reading the file.
fname	Data file to read.

Definition at line 1054 of file input.c.

Error* read_aux_input	(	Matblock_u8 **	ids_out,
		Vector_u32 **	labels_out,
		Matrix_i32 **	markers_out,
		const char *	fname
	)

Reads the IDs, haplo labels and markers from an auxiliary file.

Parameters:

ids_out	Result parameter. If opts.id_cols is zero *ids_out will be NULL.
labels_out	Result parameter. If opts.labels_col is zero *labels_out will be NULL.
markers_out	Result parameter. Will always be defined, unless there was an error reading the file.
fname	Data file to read.

Definition at line 1109 of file input.c.

Error* impute_missing_markers_from_avg	(	const Vector_u32 *	imp_labels,
		Matrix_i32 *	imp_markers,
		const Vector_u32 *	src_labels,
		const Matrix_i32 *	src_markers
	)

Imputes missing marker values (zero) with their label-dependent mean value.

Parameters:

imp_labels	Labels to use for selecting samples to impute markers from.
imp_markers	Marker values of zero are imputed.
src_labels	Labels to use for selecting samples to impute markers from.
src_markers	Markers to use for imputing values.

Note:

The imputed and source sets can be the same.

Definition at line 1208 of file input.c.

Error* impute_from_parent_of_haplogroup_index	(	uint32_t	haplo_group_index,
		uint32_t	marker_no,
		uint32_t	sample_no,
		Matrix_i32 *	marker_sums,
		Matrix_i32 *	imp_markers
	)

imputes a given marker with the values from the parent haplogroup this happens when we have only one sample with a given haplogroup

Error* impute_missing_markers_from_nn	(	Matrix_i32 *	imp_markers,
		const Matrix_i32 *	src_markers
	)

Imputes missing marker values (zero) from nearest neighbor interpolation.

Parameters:

imp_markers	Marker values of zero are imputed.
src_markers	Markers to use for imputing values.

Note:

The imputed and source sets can be the same.

Definition at line 1301 of file input.c.