find.mono.repeats: Find Mono-nucleotide Repeats
In MSIseq: Assess Tumor Microsatellite Instability with a Decision Tree Classifier from Exome Somatic Mutations

This function reads in a file with multiple fasta records and find the mononucleotide repeats in the text.

1	find.mono.repeats(text, min.len = 5)

`text`	The return object from function `read.fasta`.
`min.len`	The minimum length of the mononucleotide repeats searched by the function.

This function find the mononucleotide repeats in the text and return a data frame with the following columns.

chr: a character vector that indicates the chromosome identifier with the "chr" prefix: "chr1", "chr2", ..., "chr22", "chrX", "chrY"
start: a numeric vector that indicates the start position in the chromosome
stop: a numeric vector that indicates the end position in the chromosome

A data frame with 3 columns that are the 3 variables listed above.

Mini Huang

MSIseq documentation built on May 2, 2019, 7:23 a.m.

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