Description Usage Arguments Value
Finds peak heights and permuatation peak heights for one segment
1 2 3 | maxes_1seg(dat.file, pheno.file, s0, zmin, seed, n.perm,
save.perm.stats = FALSE, segment.bounds = NULL, out.file = NULL,
max1.file = NULL, z0 = zmin * 0.3, bandwidth = 50, maxit = 50)
|
dat.file |
Data file. Should have first column as position and a header giving sample names. One row per base pair. |
pheno.file |
Phenotype file. First column should correspond to the header of dat.file. |
s0 |
Variance inflation constant. |
zmin |
Lower bound on significance thresholds. |
seed |
Set a seed for running permutations (Required) |
n.perm |
Number of permutations |
save.perm.stats |
Do you want to save all the permutation statistics? |
segment.bounds |
Length 2 vector giving start and stop base-pair for the segment. If NULL, all base-pairs in dat.file are used. |
out.file |
Output file (optional). If NULL will append "_mx.RData" to the leading portion of the dat.file name. |
max1.file |
File with data from running with n.perm=0 |
z0 |
Reference level for merging |
bandwidth |
Smoother bandwidth. |
maxit |
Maximum iterations for rlm. |
Saves an RData file with maxes list and other info. Returns the length of that list.
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