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:
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).
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).