iHS calculation in R

1. iHS.R
secondmath
Tue Oct 28 20:23:05 2014
############## 2014 SNU GEPI population genetics by Jinseob Kim ###################
############## 2. EHH, iHS calculation ##################################################
## Load package & Set directory
#install.packages("rehh")
library(rehh)
## Loading required package: gplots
##
## Attaching package: 'gplots'
##
## The following object is masked from 'package:stats':
##
## lowess
setwd("/home/secondmath/Dropbox/GSPH/myteaching/pop_gene/2012")
## Read example file, chr=12: 1424 SNPs & 280 haplotype
a=data2haplohh(hap_file="prac_hap.hap",map_file="prac_map.inp",min_maf=0,chr=12)
## Map file seems OK: 1424 SNPs declared for chromosome 12
## Standard rehh input file assumed
## Data consists of 280 haplotypes and 1424 SNPs
## EHH
par(mfrow=c(1,2))
res1=calc_ehh(a,mrk=456,limhaplo=2,limehh=0.05,plotehh=TRUE,main_leg="EHH plot")
res11=calc_ehhs(a,mrk=456,limhaplo=2,limehh=0.05,plotehh=TRUE,main_leg="EHHS plot") # site EHH
1

2. 2.6e+07 2.8e+07 3.0e+07
0.00.20.40.60.81.0
EHH plot
Position
EHH
Anc. Allele
Der. Allele
2.6e+07 2.8e+07 3.0e+07
0.20.40.60.81.0
EHHS plot
Position
EHHS
## Integrated EHH
res2=scan_hh(a) # a: ancestral, d: derived, IES: average of IHHa & IHHd (squared allele
head(res2)
## CHR POSITION FREQ_a IHHa IHHd IES
## F1200140 12 79823 0.1500000 135102.2 68522.91 69777.21
## F1200150 12 125974 0.4071429 161680.3 107183.15 123610.30
## F1200170 12 175087 0.3571429 157333.1 155777.56 156094.80
## F1200180 12 219152 0.2214286 250037.4 159839.73 166333.27
## F1200190 12 256896 0.1750000 466071.8 173269.33 184501.30
## F1200210 12 316254 0.3892857 292077.5 228681.21 246790.48
## iHS
ihs_res2=ihh2ihs(res2)
head(ihs_res2$res.ihs) ## iHS & pvalue
## CHR POSITION iHS Pvalue
## F1200140 12 79823 0.3222762 0.12653788
## F1200150 12 125974 0.8177351 0.38351558
## F1200170 12 175087 -0.1370753 0.05013628
## F1200180 12 219152 0.7830146 0.36289214
## F1200190 12 256896 1.7890234 1.13305700
## F1200210 12 316254 0.6819630 0.30516469
ihs_res2$summary.class ## summary per alle freq bin.
## Freq Class Size Mean iHH SD iHH
2

3. ## [1,] "0.05 - 0.075" "60" "0.777287796382857" "0.737413595194812"
## [2,] "0.075 - 0.1" "52" "0.435963216395243" "0.641021685121639"
## [3,] "0.1 - 0.125" "53" "0.332371980508715" "0.494815167465929"
## [4,] "0.125 - 0.15" "56" "0.49169123696354" "0.580781486711665"
## [5,] "0.15 - 0.175" "36" "0.338272919812911" "0.557299171859519"
## [6,] "0.175 - 0.2" "38" "0.18372872314435" "0.450393024202394"
## [7,] "0.2 - 0.225" "37" "0.156221814866492" "0.371917601032433"
## [8,] "0.225 - 0.25" "36" "0.324937638464128" "0.491539213848196"
## [9,] "0.25 - 0.275" "35" "0.198821549387942" "0.53358843127552"
## [10,] "0.275 - 0.3" "30" "0.0277095221301871" "0.549619811280544"
## [11,] "0.3 - 0.325" "42" "0.168813465351846" "0.512617332536968"
## [12,] "0.325 - 0.35" "47" "0.212561823991102" "0.334091037846137"
## [13,] "0.35 - 0.375" "35" "0.0778960787783505" "0.495788198190895"
## [14,] "0.375 - 0.4" "34" "0.0142114538338362" "0.337963648645465"
## [15,] "0.4 - 0.425" "37" "-0.0135618204249136" "0.519292818010164"
## [16,] "0.425 - 0.45" "29" "0.146848067738759" "0.387610402411398"
## [17,] "0.45 - 0.475" "34" "0.023234914963773" "0.462855711456721"
## [18,] "0.475 - 0.5" "22" "-0.0280038381405699" "0.597672428815518"
## [19,] "0.5 - 0.525" "21" "0.0676757215676396" "0.397285061426881"
## [20,] "0.525 - 0.55" "22" "-0.0119346374773765" "0.475444749317303"
## [21,] "0.55 - 0.575" "23" "-0.119650040006845" "0.456309312077108"
## [22,] "0.575 - 0.6" "27" "-0.208393804329524" "0.627878921699334"
## [23,] "0.6 - 0.625" "31" "-0.175432335220113" "0.431580562389071"
## [24,] "0.625 - 0.65" "31" "-0.114913122059472" "0.362470027772815"
## [25,] "0.65 - 0.675" "21" "0.0183870416195869" "0.545114444067057"
## [26,] "0.675 - 0.7" "37" "-0.241776665581487" "0.445729962977197"
## [27,] "0.7 - 0.725" "18" "-0.262633365184881" "0.314960709993038"
## [28,] "0.725 - 0.75" "24" "-0.276070830019936" "0.406614904878564"
## [29,] "0.75 - 0.775" "29" "-0.344832955793417" "0.475726025499208"
## [30,] "0.775 - 0.8" "19" "-0.326154359766926" "0.437583935197108"
## [31,] "0.8 - 0.825" "28" "-0.197815151810967" "0.61906090927441"
## [32,] "0.825 - 0.85" "26" "-0.407636344735006" "0.591045435108097"
## [33,] "0.85 - 0.875" "20" "-0.116549521453988" "0.597016190918244"
## [34,] "0.875 - 0.9" "42" "-0.374897066174067" "0.508197119111094"
## [35,] "0.9 - 0.925" "29" "-0.796408081584825" "0.804739382631854"
## [36,] "0.925 - 0.95" "36" "-0.693833406890539" "0.639986265748046"
ihsplot(ihs_res2$res.ihs) ## iHS plot: y- pvalue, x-bp
3

4. −4
−2
0
2
iHS
Chromosome
iHS
12
0
1
2
3
4
Pvalue
Chromosome
−log10[1−2|ΦiHS−0.5|]
12
## Rsb & iHS : using wgscan example's result
data(wgscan.cgu) ; data(wgscan.eut) ## Load example result
head(wgscan.cgu)
## BTA POSITION Freq_1 IHH_1 IHH_2 IES
## F0100190 1 113642 0.5429 319186.5 395166.8 350741.0
## F0100220 1 244699 0.2607 465943.5 377422.8 385189.1
## F0100250 1 369419 0.2964 518137.2 372117.0 396350.0
## F0100270 1 447278 0.1071 742502.6 318958.0 323906.8
## F0100280 1 487654 0.3857 542176.3 364969.2 412955.4
## F0100290 1 524507 0.8429 375305.8 572230.2 380989.9
head(wgscan.eut)
## BTA POSITION Freq_1 IHH_1 IHH_2 IES
## F0100190 1 113642 0.3528 331082.8 340341.6 338224.1
## F0100220 1 244699 0.3264 382078.2 434030.9 424800.2
## F0100250 1 369419 0.1226 416906.0 372273.8 372756.1
## F0100270 1 447278 0.4208 662485.5 337043.8 436346.3
## F0100280 1 487654 0.2321 458545.6 379588.7 386265.6
## F0100290 1 524507 0.8396 393546.0 526026.7 399238.6
res.rsb=ies2rsb(wgscan.cgu,wgscan.eut,"CGU","EUT") ## Rsb: Compare 2 population
head(res.rsb$res.rsb)
## BTA POSITION rSB (CGU vs EUT) Pvalue (bilateral)
## F0100190 1 113642 -0.3653553 0.14578738
4

5. ## F0100220 1 244699 -0.9188850 0.44592808
## F0100250 1 369419 -0.2621161 0.10059980
## F0100270 1 447278 -1.7440674 1.09072568
## F0100280 1 487654 -0.2396774 0.09120393
## F0100290 1 524507 -0.7081588 0.31980358
rsbplot(res.rsb$res.rsb) ## Rsb plot
−5
0
5
rSB (CGU vs EUT)
Chromosome
rSB
1 4 7 11 17 24
0
2
4
6
8
10
12
14
Pvalue
Chromosome
−log10[1−2|ΦrSB−0.5|]
1 4 7 11 17 24
## all chr iHS plot in wgscan.cgu data
ihs_res3=ihh2ihs(wgscan.cgu)
ihsplot(ihs_res3$res.ihs)
5

6. −6
−4
−2
0
2
4
iHS
Chromosome
iHS
1 4 7 11 17 24
0
2
4
6
8
Pvalue
Chromosome
−log10[1−2|ΦiHS−0.5|]
1 4 7 11 17 24
6