processLastAlignedBase: processLastAlignedBase
In adamstruck/RECD: Repeat Exansion & Contraction Detection

Description Usage Arguments Details Value Author(s)

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

  processLastAlignedBase(con, table_name, input_file,
    imd_dist = NULL, upper_limit = 0.95,
    margin = (read_length/2), read_length = 75,
    min_repeat_length = (read_length/2), output_dir = ".",
    overwrite = FALSE, append_chr = TRUE)

`con`	database connection
`table_name`	name of table in database
`input_file`	last_aligned_base.tsv file
`imd_dist`	.insert_len_dist file (i.e. the inner mate distance distribution 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. Facing reads whose ends are farther from the repeat than the value set by this parameter will be not be used. [default= 0.95]
`read_length`	read length [default= 75]
`output_dir`	output directory to write results [default= "."]
`overwrite`	overwrite output files if they exist [default= FALSE]
`append_chr`	appends "chr" to chromosome names of inner_mate_ranges file [default= TRUE]
`max_gap`	maximum distance between the last aligned base and the start or end of the repeat [default = 500]
`margin`	maximum bp overlap between each read and a given repeat repeat [default= read_length/2]
`min_repeat_length`	minimum repeat length in reference genome [default= read_length/2]

Description of output files: 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)

_facing, and _fully_repetitive tsv files

Adam Struck - Intern

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