Sib-pair Command: frequencies | describe


ClassAnalysis and data manipulation command
Namefrequencies | 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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