snipar.scripts.correlate module

Infers correlations between direct effects and population effects, and between direct effects and average non-transmitted coefficients (NTCs). Minimally: the script requires summary statistics as output by snipar’s gwas.py script, and either LD-scores (as output by snipar’s ibd.py script or LDSC) or .bed files from which LD-scores can be computed Args:

‘-h’, ‘–help’, default===SUPPRESS==

show this help message and exit

: str

Address of sumstats files in SNIPar sumstats.gz text format (without .sumstats.gz suffix). If there is a @ in the address, @ is replaced by the chromosome numbers in chr_range (optional argument)

‘–chr_range’

number of the chromosomes to be imputed. Should be a series of ranges with x-y format or integers.

: str

Prefix for output file(s)

‘–ldscores’str

Address of ldscores as output by LDSC

‘–bed’str

Address of observed genotype files in .bed format (without .bed suffix). If there is a # in the address, # is replaced by the chromosome numbers in the range of 1-22.

‘–threads’int

Number of threads to use for IBD inference. Uses all available by default.

‘–min_maf’float, default=0.05

Ignore SNPs with minor allele frequency below min_maf (default 0.05)

‘–corr_filter’float, default=6.0

Filter out SNPs with outlying sampling correlations more than corr_filter SDs from mean (default 6)

‘–n_blocks’int, default=200

Number of blocks to use for block-jacknife variance estimate (default 200)

‘–save_delete’

Save jacknife delete values

‘–ld_wind’float, default=1.0

The window, in cM, within which LD scores are computed (default 1cM)

‘–ld_out’str

Output LD scores in LDSC format to this address

Results:

correlations

A text file containing the estimated correlations and their standard errors.

snipar.scripts.correlate.main(args)

“Calling this function with args is equivalent to running this script from commandline with the same arguments. Args:

args: list

list of all the desired options and arguments. The possible values are all the values you can pass this script from commandline.