check_chr {MungeSumstats} | R Documentation |
Ensure all SNPs on specified chromosomes are removed
check_chr( sumstats_dt, path, rmv_chr, log_folder_ind, check_save_out, tabix_index, nThread, log_files, make_uppercase = TRUE, rmv_chrPrefix = TRUE )
path |
Filepath for the summary statistics file to be formatted. A dataframe or datatable of the summary statistics file can also be passed directly to MungeSumstats using the path parameter. |
rmv_chr |
vector or character The chromosomes on which the SNPs should be removed. Use NULL if no filtering necessary. Default is X, Y and mitochondrial. |
log_folder_ind |
Binary Should log files be stored containing all filtered out SNPs (separate file per filter). The data is outputted in the same format specified for the resulting sumstats file. The only exception to this rule is if output is vcf, then log file saved as .tsv.gz. Default is FALSE. |
tabix_index |
Index the formatted summary statistics with tabix for fast querying. |
nThread |
Number of threads to use for parallel processes. |
log_files |
list of log file locations |
rmv_chrPrefix |
Remove "chr" or "CHR" from chromosome names. Default is TRUE. |
list containing sumstats_dt, the modified summary statistics data table object and the log file list