Used in: gor/nor

RANK

The RANK command returns the rank of a number within a set of numbers. It compares the value of each cell in the specified column to all the values in the result set and returns the rank of that row in a column labelled “rank_<column_name>”.

The RANK command has two necessary parameters, namely the binsize, which can be set to “chrom”, “genome” or to a numeric value. The column specified in the RANK command must be a numeric column.

Using RANK in a nor query will give an error if binsize input parameter is used.

Usage

gor ... | RANK binsize column [ attributes ]

nor ... | RANK column [ attributes ]

Options

-o asc | desc

Rank order. By default it is descending.

-q

Report rank distribution, lower rank and equal.

-z

Report z-value = (x-mean)/std.

-c

Report the total count for the bin.

-b

Report the value where the rank is 1.

-rmax number

Report only rows where rank <= number.

-gc cols

Grouping columns (other than bin).

Examples

The example below takes some entries from the #dbsnp# table with indels of some length, calculates the length of the reference column in the row and then ranks the value in the column.

gor #dbsnp# | WHERE len(reference) > 4 OR len(allele) > 4
   | CALC refLength len(reference) | PREFIX refLength calc | TOP 6
   | RANK genome calc_refLength
../_images/RANK.png

The following query will perform a parallelised gor query that calculates the length of each gene and then ranks them by length and returns the longest gene on each chromosome.

pgor #genes#
   | calc length (gene_end - gene_start)
   | rank chrom length -o desc
   | where rank_length = 1

The next query will return the shortest gene:

pgor #genes#
   | calc length (gene_end - gene_start)
   | rank chrom length -o asc
   | where rank_length = 1