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Sliding Window frequency (version 5.0.0)
A tabular file with eQTL and gene frequencies for each interval.
A tabular file number of cM, bp, inteval positions and bins on each chromosome.
A tabular file with the total number of genes, eQTLs, cM and number of permutations.

What it does

Combine x cM intervals (size of lookup bins; for example 2 cM), to be used in a sliding window approach.

For 2 cM lookup bins:

• For two intervals per sliding window, intervals smaller than 2 cM are combined with its two flanking 2 cM intervals.

Calculate the number of eQTLs per sliding window (4 - 5.9 cM intervals).

Calculate the number of genes per sliding window (4 - 5.9 cM intervals).

• For three intervals per sliding window, intervals smaller than 2 cM are combined with 3 flanking 2 cM intervals.

Calculate the number of eQTLs per sliding window (6 - 7.9 cM intervals).

Calculate the number of genes per sliding window (6 - 7.9 cM intervals).

Example input files

Frequency per bin file: frequency of all, cis and trans eQTLs and genes, each row correspond to a 2cM (or smaller) interval (11 columns; only a part of the file is shown):

```int.id  chr     marker  interval        cM      bp        length_cM    num.eQTL.all    num.eQTL.cis    num.eQTL.trans  num.genes
1       1       1       0.0001         0.0     2038278         2.0     94.0            2.0             64.0            12.0
2       1       1       0.0201         2.0     2466324         2.0     17.0            3.0             11.0            34.0
3       1       1       0.0401         4.0     2894370         2.0     8.0             2.0             5.0             29.0
4       1       1       0.0601         6.0     3322416         1.53    11.0            5.0             3.0             10.0
5       1       2       0.0754         7.53    3649871         2.0     27.0            6.0             19.0            18.0
6       1       2       0.0954         9.53    4095673         2.0     8.0             4.0             3.0             12.0
7       1       2       0.1154         11.53   4541476         2.0     4.0             2.0             2.0             17.0
8       1       2       0.1354         13.53   4987278         2.0     8.0             4.0             2.0             19.0
9       1       2       0.1554         15.53   5433081         2.0     5.0             0               3.0             15.0
```

Chromosome summary file, each row correspond to a chromosome (6 columns; only a part of the file is shown). The last row gives the total across the genome:

```chr    markers cM      bp      int_positions   bins
1      27      324.4   301354135       177     176
2      14      169.11  237068873       92      91
3      19      221.29  232140174       123     122
4      20      188.37  241473504       105     104
5      20      203.82  217872852       110     109
6      17      195.85  169174353       106     105
Total  117     1302.84 1399083891      713     707
```

Frequency summary file (2 columns):

```Total number of eQTLs (all)             31549
Total number of cis-eQTLs               4863
Total number of trans-eQTLs             21428
Total number of genes                   31036
Total number of cM                      1861.57
Expected number of eQTL per cM (all)    16.95
Expected number of cis-eQTL per cM      2.61
Expected number of trans-eQTL per cM    11.51
Expected number of genes per cM         16.67
User specified number of permutations   1000
Number of intervals per sliding window  2
```

Example output files

Sliding frequency file: Frequency of eQTLs and genes per sliding window interval (4 - 5.9 cM) output file, each row correspond to a sliding window interval (11 columns; only a part of the file is shown):

```sliding.id  chr  sliding.cM   sliding.all.eQTL  sliding.cis.eQTL  sliding.trans.eQTL  sliding.genes  sliding.all.eQTL/cM sliding.cis.eQTL/cM  sliding.trans.eQTL/cM   sliding.genes/cM
1              1       4.0             111.0           5.0             75.0            46.0            27.75                   1.25            18.75                   11.5
2              1       4.0             25.0            5.0             16.0            63.0            6.25                    1.25            4.0                     15.75
3              1       5.53            46.0            13.0            27.0            57.0            8.32                    2.35            4.88                    10.31
4              1       4.0             35.0            10.0            22.0            30.0            8.75                    2.5             5.5                     7.5
5              1       4.0             12.0            6.0             5.0             29.0            3.0                     1.5             1.25                    7.25
6              1       4.0             12.0            6.0             4.0             36.0            3.0                     1.5             1.0                     9.0
7              1       4.0             13.0            4.0             5.0             34.0            3.25                    1.0             1.25                    8.5
8              1       5.24            67.0            5.0             46.0            41.0            12.79                   0.95            8.78                    7.82
9              1       4.0             57.0            5.0             39.0            53.0            14.25                   1.25            9.75                    13.25
10             1       4.0             13.0            3.0             9.0             58.0            3.25                    0.75            2.25                    14.5
11             1       4.0             11.0            3.0             5.0             54.0            2.75                    0.75            1.25                    13.5
12             1       4.0             11.0            4.0             3.0             35.0            2.75                    1.0             0.75                    8.75
```

Map sliding window IDs (first column) to lookup table IDs (second column) (2 columns; only a part of the file is shown):

```1      [1, 2]
2      [2, 3]
3      [3, 4, 5]
4      [5, 6]
5      [6, 7]
6      [7, 8]
7      [8, 9]
8      [9, 10, 11]
9      [11, 12]
10     [12, 13]
11     [13, 14]
12     [14, 15]
13     [15, 16]
14     [16, 17]
15     [17, 18]
16     [18, 19]
17     [19, 20, 21]
```

Frequency per cM plot of cis-eQTL, trans-eQTL and genes (in pdf format, produced using R).