syntheticNucMapFromDistValidation: Parameter validation for the 'syntheticNucMapFromDist'...
In nucleoSim: Generate synthetic nucleosome maps

Description Usage Arguments Value Author(s) Examples

View source: R/nucleoSimInternFunctions.R

Validate that all values passed to the function are formated for the syntheticNucMapFromDist function.

1 2	syntheticNucMapFromDistValidation(wp.num, wp.del, wp.var, fuz.num, fuz.var, max.cover, nuc.len, len.var, lin.len, rnd.seed, as.ratio)

`wp.num`	a non-negative `integer`, the number of well-positioned (non overlapping) nucleosomes.
`wp.del`	a non-negative `integer`, the number of well-positioned nucleosomes to remove to create uncovered regions.
`wp.var`	a non-negative `integer`, the variance of the starting position of the sequences associated with well-positioned nucleosomes. This parameter introduces some variation in the starting position of the sequences describing a nucleosome.
`fuz.num`	a non-negative `integer`, the number of fuzzy nucleosomes. Those nucleosomes can overlap other well-positioned or fuzzy nucleosomes.
`fuz.var`	a non-negative `integer`, the variance of the fuzzy nucleosomes. This variance can be different than the one used for the well-positioned nucleosome reads.
`max.cover`	a positive `integer`, the maximum coverage for one nucleosome. The final coverage can have a higher value than `max.cover` since reads from differents nucleosomes can be overlapping.
`nuc.len`	a non-negative `integer`, the nucleosome length.
`len.var`	a non-negative `integer`, the variance of the distance between a forward read and its paired reverse read.
`lin.len`	a non-negative `integer`, the length of the DNA linker DNA.
`rnd.seed`	a single value, interpreted as an `integer`, or `NULL`. If a `integer` is given, the value is used to set the seed of the random number generator. By fixing the seed, the generated results can be reproduced.
`as.ratio`	a `logical`, if `TRUE`, a synthetic naked DNA control map is created and the ratio between it and the nucleosome coverage are calculated. It can be used to simulate hybridization ratio data, like the one in Tiling Arrays. Both control map and calculated ratio are returned.

0 indicating that all parameters validations have been successful.

Astrid Deschenes

## The function returns 0 when all paramaters are valid
nucleoSim:::syntheticNucMapFromDistValidation(wp.num = 20, wp.del = 2,
wp.var = 3, fuz.num = 10, fuz.var = 5, max.cover = 100, nuc.len = 147,
len.var = 4, lin.len = 40, rnd.seed = 201, as.ratio = FALSE)

## The function raises an error when at least one paramater is not valid
## Not run: nucleoSim:::syntheticNucMapFromDistValidation(wp.num = -1,
wp.del = 2, wp.var = 3, fuz.num = 10, fuz.var = 5, max.cover = 100,
nuc.len = 147, len.var = 4, lin.len = 40, rnd.seed = 201, as.ratio = FALSE)
## End(Not run)
## Not run: nucleoSim:::syntheticNucMapFromDistValidation(wp.num = 20,
wp.del = 2, wp.var = -3, fuz.num = 10, fuz.var = 5, max.cover = 100,
nuc.len = 147, len.var = 4, lin.len = 40, rnd.seed = 201, as.ratio = FALSE)
## End(Not run)