ghap.freq | R Documentation |
This function takes a GHap.phase object and computes the allele frequency for each marker.
ghap.freq(object, type = "maf", only.active.samples = TRUE, only.active.markers = TRUE, ncores = 1, verbose = TRUE)
object |
A GHap object of type phase or plink. |
type |
A character value indicating which allele frequency to compute. Valid options are minor allele frequency ('maf', default), frequency of allele 0 ('A0') and frequency of allele 1 ('A1'). |
only.active.samples |
A logical value specifying whether only active samples should be used for calculations (default = TRUE). |
only.active.markers |
A logical value specifying whether only active markers should be included in the output (default = TRUE). |
ncores |
A numeric value specifying the number of cores to be used in parallel computing (default = 1). |
verbose |
A logical value specfying whether log messages should be printed (default = TRUE). |
The function outputs a numeric vector of the same length of active markers containing allele frequencies based on the active samples.
Yuri Tani Utsunomiya <ytutsunomiya@gmail.com>
Marco Milanesi <marco.milanesi.mm@gmail.com>
# #### DO NOT RUN IF NOT NECESSARY ### # # # Copy phase data in the current working directory # exfiles <- ghap.makefile(dataset = "example", # format = "phase", # verbose = TRUE) # file.copy(from = exfiles, to = "./") # # # Copy plink data in the current working directory # exfiles <- ghap.makefile(dataset = "example", # format = "plink", # verbose = TRUE) # file.copy(from = exfiles, to = "./") # # ### RUN ### # # # Calculate allele frequency for phase data # phase <- ghap.loadphase("example") # q <- ghap.freq(phase, type = 'A0') # p <- ghap.freq(phase, type = 'A1') # maf <- ghap.freq(phase, type = 'maf') # # # Calculate allele frequency for plink data # plink <- ghap.loadplink("example") # q <- ghap.freq(plink, type = 'A0') # p <- ghap.freq(plink, type = 'A1') # maf <- ghap.freq(plink, type = 'maf')
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.