mapATR: mapATR [mapAlignmentsToRepeats]
In adamstruck/RECD: Repeat Exansion & Contraction Detection

Description Usage Arguments Details Value Author(s)

Sorts read pairs into three categories: flanking, facing, and fully repetitive.

  mapATR(con, table_name, input_file, imd_dist = NULL,
    upper_limit = 0.95, margin = (read_length/4),
    read_length, min_repeat_length = 12, output_dir = ".",
    append_chr = FALSE, overwrite = TRUE)

`con`	database connection
`table_name`	name of table in database
`input_file`	inner_mate_range.tsv file (make sure chr names are compatible with your database)
`imd_dist`	.insert_length_dist file (i.e. the inner mate distance distribution file for the sample)
`upper_limit`	values between 0 and 1 will be used to set prob in quantile() and then used to calculate the maximum allowed distance from the repeat. Values greater than 1 will be applied as the maximum. Read pairs whose ends are farther from the repeat than the value set by this parameter will be not be used. [default= 0.95]
`margin`	minimum bp a read must be anchored outside the repeat [default= read_length/4]
`read_length`	read length
`min_repeat_length`	minimum repeat length in reference genome [default= 12]
`output_dir`	output directory to write results [default= "."]
`append_chr`	appends "chr" to chromosome names of inner_mate_ranges file if TRUE [default= TRUE]
`overwrite`	should output files be overwritten? [default= TRUE]
`margin`	maximum bp overlap between each read and a given repeat repeat [default= read_length/2]

Description of output files: flanking: read pair completely flank the repeat or are anchored outside the repeat (minimum = margin) facing: one read flanks or is anchored outside the repeat (minimum = margin) while its pair aligned inside the repeat (or didn't meet minimum anchor requirements) fully_repetitive: both reads in pair aligned inside the repeat (or didn't meet minimum anchor requirements)

_flanking, _facing, and _fully_repetitive .tsv files

Adam Struck

adamstruck/RECD documentation built on May 10, 2019, 5:51 a.m.