aSample object (RoAM Toolbox for Matlab®)

Holds information about CpG positions in ancient DNA samples. The information includes frequencies of the different nucleotides observed in each CpG position in the human reference genome, as well as some magnitudes that are computed based on these frequencies.

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Each field can be accessed by the dot (.) operation, or by the GET function. The GET function can work on multiple instances simultaneously. Most fields, except for those that are Dependent, can be modified using the dot (.) operation, or by the SET function.

		Field	Description	Type	Default	Dedicated Get/Set Function
		name	Name of sample. This field will never be empty.	string	'unknown'
		abbrev	Abbreviated name, usually used a three-letter unique identifier of the sample.	string	'unk'
		species	Taxonomic grouping of the sample.	string	'unknown'
		reference	Genomic reference against which aligment of the sample reads was done.	string	''
		library	Library preparation protocol, either 'SS' (single-stranded) or 'DS' (double-stranded).	string	''
		metadata	Additional information on the sample.	metadata structure	[]
		chr_names	List of chromosome names	cell of strings over chromosomes.	[]
		coord_per_position	Every CpG position has two C's (on the two opposing strands). If data refere to each separately, this field is 2. If the data sum the frequencies from the two positions, this field is 1.	Cx1 vector of integers over chromosomes	[]
		No_As	Frequency of A's at the CpG positions.	cell over chromosomes, a vector of counts per position for each chromosome	[]
		No_Cs	Frequency of C's at the CpG positions.	cell over chromosomes, a vector of counts per position for each chromosome	[]
		No_Gs	Frequency of G's at the CpG positions.	cell over chromosomes, a vector of counts per position for each chromosome	[]
		No_Ts	Frequency of T's at the CpG positions.	cell over chromosomes, a vector of counts per position for each chromosome	[]
		aOga	The ratio #A/(#A + #G) at the CpG positions.	cell over chromosomes, a vector per position for each chromosome	[]
		tOct	The ratio #T/(#T + #C) at the CpG positions.	cell over chromosomes, a vector per position for each chromosome	[]
		methylation	Estimated methylation at each CpG position	cell over chromosomes, a vector per position for each chromosome	[]
		drate	Estimated deamination rate	drate structure	[]
	Dependent	no_chrs	Number of chromosomes, C.Set to zero for void objects.	integer scalar	0	nosamples

Empty instance (scalar)

an empty aSample instance, with all fields initialized to their default values.

syntax: as = aSample;

Empty instance (matrix)

a vector of empty sSample instances.

syntax: as = aSample(size);

Copy constructor

one aSample instance is copied into another.

syntax: as_destination = aSample(as_origin);

Construction by field names

an instance is formed by directly providing field values. Any field which is not dependent is permitted.

syntax: as = aSample(field_name, field_value, ...);

example: as = aSample('name','Ust ''Ishim','abbrev','UST');

SET/GET functions:

bundle

sets fields from a CpG structure

get

get method

getNo_Ts

get No_Ts for a specific chromosome

set

set method