# Find the r-squared cutoff

### Description

Returns the minimum value of r2 in r2.vec that keeps the number of constraint matrix columns less than maxcol.

### Usage

1 | ```
r2.cut.fn(block.obj, block.cood, Xa, Y, maxcol, r2.cut.min, r2.cut.max, r2.vec.length)
``` |

### Arguments

`block.obj` |
An object of class gwaa.data from GenABEL. |

`block.cood` |
A vector of length p+1, where p is the number of SNPs. block.cood is an indicator vector that indicates block boundaries at all p+1 SNP bounded intervals. Use find.bounds to create this vector. |

`Xa` |
If block.obj is NA then a genotype matrix must be provided. Xa is a matrix of genotype values codes as 0, 1 or 2 for homozygous major, heterozygous, or homozygous minor, respectively. |

`Y` |
If block.obj is NA then a phenotype vector Y must be provided. Y is a vector of diagnoses, where 0 is non-diseased and 1 is diseased. |

`maxcol` |
The maximum number of columns allowed in the constraint matrix. Default is 5,000. |

`r2.cut.min` |
The lower bound of the r2.cut interval |

`r2.cut.max` |
The upper bound of the r2.cut interval |

`r2.vec.length` |
The number of r2.cut values uniformly spaced in r2.cut interval |

### Value

The function r2.cut.fn returns the minimum value of r2.cut that satsisfies, ncol(A) < maxcol, where A is the constraint matrix

### Author(s)

Samuel G. Younkin

### See Also

ld_lasso