Output sumstats in certain formats

GWASLab provides a flexible formatting and saving function.

.to_format()

.to_format(
          path="./sumstats",
          fmt="ldsc",   
          ...
          )

Options

`.to_format()` options	DataType	Description	Default
`path`	`string`	the path for the output file; only prefix is needed.	`"./sumstats"`
`fmt`	`string`	output format for sumstats. Currently support `plink` ,`plink2`, `ldsc`, `saige`, `fastgwa`, `regenie` and so forth. For details , please check https://github.com/Cloufield/formatbook.	`"gwaslab"`
`cols`	`list`	list of additional columns to linclude in the output	`None`
`extract`	`list`	a list of variant SNPIDs to include.	`None`
`exclude`	`list`	a list of variant SNPIDs to exclude.	`None`
`id_use`	`SNPID` or `rsID`	specify which ID to use when excluding or extracting variants.	`rsID`
`hapmap3`	`boolean`	If True, only output Hapmap3 SNPs.	`False`
`exclude_hla`	`boolean`	if True, exclude variants in the MHC region from the output.	`False`
`hla_range`	`tuple`	a tuple of 2 numbers (MBp) indicating the start and the end position of the HLA region.	`(25,34)`
`build`	`string`	reference genome build.	`"19"`
`xymt_number`	`boolean`	if True, output sex chromosomes as X/Y/MT	"False"
`xymt`	`list`	3-element list of sex chromosome notations to indicate how to convert integers to sex chromosome	`["X","Y","MT"]`
`chr_prefix`	`string`	Add a prefix to chromosomes. For example, 6 -> Chr6.	`""`
`bgzip`	`boolean`	If True, bgzip the output file. Only works for bed and vcf format.	-
`tabix`	`boolean`	If True, use tabix to index the bgzipped output file. Only works for bed and vcf format.	-
`tabix_indexargs`	`dict`	extra parameters for pysam.tabix_index()	`{}`
`md5sum`	`boolean`	If True, calculate and output the file MD5 hashes	`False`
`to_csvargs`	`dict`	extra parameters for pd.to_csv()	`None`
`float_formats`	`dict`	a dictionary to specify the float format for each column.	`None`
`verbose`	`boolean`	If True, print logs.	`True`
`output_log`	`boolean`	If True, save the log to a file.	`True`
`ssfmeta`	`boolean`	If True, output a gwas-ssf-style meta file.	`False`

Format dictionary

Using float_formats, you can specify the formats for numbers.

Default formats for floating-point numbers

{'EAF': '{:.4g}', 'BETA': '{:.4f}', 'Z': '{:.4f}','CHISQ': '{:.4f}','SE': '{:.4f}','OR': '{:.4f}','OR_95U': '{:.4f}','OR_95L': '{:.4f}','INFO': '{:.4f}','P': '{:.4e}','MLOG10P': '{:.4f}','DAF': '{:.4f}'}

Examples

GWASLab supports commonly used tabular formats, which are listed in a companion repository formatbook.

formatbook

For more details, please check formatbook

Example

See Output sumstats