Coding Copy Number Segments with Letters.

See get_score_matrix() for examples. See details for full description of implementation.

transform_seqs(x, simple_version = FALSE, max_len_score = 4L)

Arguments

x	a CopyNumber object or a data.frame with at least 5 columns ("sample", "chromosome", "start", "end", "segVal").
simple_version	if TRUE, just use segmental copy number value.
max_len_score	the maximum score for segment length (should >=4). The maximum score for copy number value is 6 (cannot be changed).

Value

a list.

Details

For complicated cases, letters are grouped as short (<50kb), mid (<500kb), long (<5Mb), long (or extreme) long (>5Mb) segments.

• A B C D for copy number 0.

• E F G H for copy number 1.

• I J K L for copy number 2.

• M N O P for copy number 3.

• Q R S T for copy number 4.

• U V W X for copy number 5+.

For simplified cases, letters are used to code only segment copy number value.

• A for copy number 0.

• B for copy number 1.

• C for copy number 2.

• D for copy number 3.

• E for copy number 4.

• F for copy number 5+.