hd-params.md

High dimensional data parameters

• DATA_FILE Mandatory (alternatively with DATA_FILE_PREFIX). Prefer this to DATA_FILE_PREFIX. Points to the HD data file.
• DATA_FILE_PREFIX deprecated because it doesn't behave like a prefix (unlike the original pipeline); use DATA_FILE instead.
• DATA_TYPE Mandatory; must be R (raw values) or L (log transformed values).
• LOG_BASE Default: 2. If present must be 2. The log base for calculating log values.
• SRC_LOG_BASE Has to be specified only with DATA_TYPE=L. Specifies which logarithm base was used for transforming the data values.
• MAP_FILENAME Mandatory. Filename of the mapping file.
• ALLOW_MISSING_ANNOTATIONS Default: N. Y for yes, N for no. Whether the job should be allowed to continue when the data set doesn't provide data for all the annotations (here probes).
• SKIP_UNMAPPED_DATA Default: N. If Y then it ignores data points that have no subject mapping. Otherwise (N) gives an error for such data points.
• ZERO_MEANS_NO_INFO Default: N. If Y then the rows with raw values equal 0 would be filtered out. Otherwise (N) they will be inserted to the database. The flag applies to most of HD data types. It does not effect CNV (ACGH) data. For RNAseq read count data the check on zeros happens based on normalized read count.