| Class | Analysis and data manipulation command |
| Name | frequencies | describe |
| Arguments | [[<codominant marker>| <binary trait>| <quantitative trait>]...[to]...<trait>] | snp. |
Print allele frequencies for marker loci, segregation ratios for binary trait, or means, variances, familial correlations and a sibship variance test for a quantitative trait. Default is to describe all loci. The snp option prints minor allele frequencies and number typed for all diallelic marker loci.
Example:
>> include williamsex.in >> describe >> frequencies snp
>> clear >> include mooser.in >> describe [...] ------------------------------------------------ Summary statistics for trait "Lpa" ------------------------------------------------ Descriptive Stats All Founders Nonfounders ----------------------------------------------------------- Means 5.74532 5.80971 5.71391 Variances 7.47448 7.34069 7.57302 Stand Devs 2.73395 2.70937 2.75191 Maxima 15.2315 15.2315 14.0712 Minima 0.547723 1.00000 0.547723 No. obs 305 100 205 No. missing 19 19 0 -------------- Familial correlations (pairwise) -------------- Rel 1 Rel 2 Std Dev 1 Std Dev 2 Correlation N Pairs Jack Cor JSE -------------------------------------------------------------- -------------- Husband Wife 2.6023 2.9374 -0.0292 48 -0.0283 0.2250 Gparent Gchild 2.5410 2.8246 0.7329 24 0.7267 0.2882 Halfsib Hsib 2.5425 -0.1901 20 -0.1906 0.4018 Avuncular 2.1560 2.3243 0.6493 39 0.6431 0.3283 Full Cousins 2.0186 0.3225 27 0.3089 0.6387 Parent Off 2.7602 2.7081 0.4825 358 0.4819 0.0776 Fullsib Fsib 2.8698 0.5485 267 0.5481 0.0817 Father Son 2.3111 2.3953 0.5518 71 0.5520 0.1368 Father Dau 2.5426 2.8745 0.4586 82 0.4591 0.1327 Mother Son 2.7248 2.5828 0.5032 95 0.5017 0.1707 Mother Dau 3.1667 2.9001 0.4642 110 0.4630 0.1259 Brothers 2.3333 0.6402 58 0.6388 0.1276 Sisters 2.9873 0.4809 74 0.4790 0.1634 Brother-Sister 3.0191 2.9529 0.5525 135 0.5526 0.0979 Jackknife random subsample = delete-10 Number of samples = 1000 WLS estimates of heritability (approx SE) Heritability = 1.0363 (0.0163) Dominance (d2)= 0.1214 (0.0480)
>> clear >> include melaexpression.in >> keep 1 -- 10 >> freq snps Marker NAll Allele(s) Freq Het Ntyped -------------------- ---- ----------- ------ ------ ------ rs6576700 2 A (B) 0.4500 0.5077 20 SNP_A-1780419 [A/G] rs7730126 2 A (B) 0.3182 0.4440 22 SNP_A-1780415 [A/G] rs10834942 2 B (A) 0.1667 0.2874 15 SNP_A-1780413 [A/G] rs7995987 2 A (B) 0.3636 0.4736 22 SNP_A-1780379 [G/T] rs7828844 2 A (B) 0.2273 0.3594 22 SNP_A-1780378 [A/G] rs11040883 2 A (B) 0.1136 0.2061 22 SNP_A-1780377 [A/G] rs2024406 2 B (A) 0.3636 0.4736 22 SNP_A-1780375 [A/G] rs515983 2 A (B) 0.4318 0.5021 22 SNP_A-1780374 [A/G] rs2287407 2 A (B) 0.2045 0.3330 22 SNP_A-1780373 [A/G]
Use the recode command to rename alleles from A/B to those in the annotation, and relist:
>> recode $m nuc >> freq snps Marker NAll Allele(s) Freq Het Ntyped -------------------- ---- ----------- ------ ------ ------ rs6576700 2 A (G) 0.4500 0.5077 20 SNP_A-1780419 [A/G] rs7730126 2 A (G) 0.3182 0.4440 22 SNP_A-1780415 [A/G] rs10834942 2 G (A) 0.1667 0.2874 15 SNP_A-1780413 [A/G] rs7995987 2 G (T) 0.3636 0.4736 22 SNP_A-1780379 [G/T] rs7828844 2 A (G) 0.2273 0.3594 22 SNP_A-1780378 [A/G] rs11040883 2 A (G) 0.1136 0.2061 22 SNP_A-1780377 [A/G] rs2024406 2 G (A) 0.3636 0.4736 22 SNP_A-1780375 [A/G] rs515983 2 A (G) 0.4318 0.5021 22 SNP_A-1780374 [A/G] rs2287407 2 A (G) 0.2045 0.3330 22 SNP_A-1780373 [A/G]
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