Remove highly correlated variables from a data frame or matrix
HI Jim, This: colnames(calc.jim)[colSums(abs(calc.jim)>0.8)<3] was the master take! Thank you so much!!!
On Thu, Nov 14, 2019 at 3:39 PM Jim Lemon <drjimlemon at gmail.com> wrote:
I thought you were going to trick us. What I think you are asking now
is how to get the variable names in the columns that have at most one
_absolute_ value greater than 0.8. OK:
# I'm not going to try to recreate your correlation matrix
calc.jim<-matrix(runif(100,min=-1,max=1),nrow=10)
for(i in 1:10) calc.jim[i,i]<-1
rownames(calc.jim)<-<-colnames(calc.jim)<-paste0("rs",1:10)
Now that we have a plausible fake correlation matrix, all we have to
do is extract the column names:
colnames(calc.jim)[colSums(abs(calc.jim)>0.8)<2]
Of course, what you really meant could have been, "I want the column
names of the variables with at most one absolute value greater than
0.8 ignoring the diagonal values because I don't care about those". If
so:
colnames(calc.jim)[colSums(abs(calc.jim)>0.8)<3]
Any more tricks?
Jim
On Fri, Nov 15, 2019 at 8:17 AM Ana Marija <sokovic.anamarija at gmail.com> wrote:
what would be the approach to remove variable that has at least 2 correlation coefficients >0.8? this is the whole output of the head()
head(calc.rho)
rs56192520 rs3764410 rs145984817 rs1807401 rs1807402 rs35350506
rs56192520 1.000 0.976 0.927 0.927 0.927 0.927
rs3764410 0.976 1.000 0.952 0.952 0.952 0.952
rs145984817 0.927 0.952 1.000 1.000 1.000 1.000
rs1807401 0.927 0.952 1.000 1.000 1.000 1.000
rs1807402 0.927 0.952 1.000 1.000 1.000 1.000
rs35350506 0.927 0.952 1.000 1.000 1.000 1.000
rs2089177 rs12325677 rs62064624 rs62064631 rs2349295 rs2174369
rs56192520 0.927 0.927 0.927 0.927 0.709 0.903
rs3764410 0.952 0.952 0.952 0.952 0.728 0.928
rs145984817 1.000 1.000 1.000 1.000 0.771 0.975
rs1807401 1.000 1.000 1.000 1.000 0.771 0.975
rs1807402 1.000 1.000 1.000 1.000 0.771 0.975
rs35350506 1.000 1.000 1.000 1.000 0.771 0.975
rs7218554 rs62064634 rs4360974 rs4527060 rs6502526 rs6502527
rs56192520 0.903 0.903 0.903 0.903 0.903 0.903
rs3764410 0.928 0.928 0.928 0.928 0.928 0.928
rs145984817 0.975 0.975 0.975 0.975 0.975 0.975
rs1807401 0.975 0.975 0.975 0.975 0.975 0.975
rs1807402 0.975 0.975 0.975 0.975 0.975 0.975
rs35350506 0.975 0.975 0.975 0.975 0.975 0.975
rs9900318 rs8069906 rs9908521 rs9908336 rs9908870 rs9895995
rs56192520 0.903 0.268 0.327 0.327 0.327 0.582
rs3764410 0.928 0.276 0.336 0.336 0.336 0.598
rs145984817 0.975 0.309 0.371 0.371 0.371 0.638
rs1807401 0.975 0.309 0.371 0.371 0.371 0.638
rs1807402 0.975 0.309 0.371 0.371 0.371 0.638
rs35350506 0.975 0.309 0.371 0.371 0.371 0.638
rs7211086 rs9905280 rs8073305 rs8072086 rs4312350 rs4313843
rs56192520 0.880 0.268 0.327 0.880 0.880 0.880
rs3764410 0.905 0.276 0.336 0.905 0.905 0.905
rs145984817 0.951 0.309 0.371 0.951 0.951 0.951
rs1807401 0.951 0.309 0.371 0.951 0.951 0.951
rs1807402 0.951 0.309 0.371 0.951 0.951 0.951
rs35350506 0.951 0.309 0.371 0.951 0.951 0.951
rs8069610 rs883504 rs8072394 rs4280293 rs4465638 rs12602378
rs56192520 0.582 0.903 0.582 0.582 0.811 0.302
rs3764410 0.598 0.928 0.598 0.598 0.836 0.311
rs145984817 0.638 0.975 0.638 0.638 0.879 0.344
rs1807401 0.638 0.975 0.638 0.638 0.879 0.344
rs1807402 0.638 0.975 0.638 0.638 0.879 0.344
rs35350506 0.638 0.975 0.638 0.638 0.879 0.344
rs9899059 rs6502530 rs4380085 rs6502532 rs4792798 rs4792799
rs56192520 0.302 0.309 0.834 0.251 0.063 0.063
rs3764410 0.311 0.318 0.858 0.259 0.080 0.080
rs145984817 0.344 0.352 0.902 0.291 0.086 0.086
rs1807401 0.344 0.352 0.902 0.291 0.086 0.086
rs1807402 0.344 0.352 0.902 0.291 0.086 0.086
rs35350506 0.344 0.352 0.902 0.291 0.086 0.086
rs4316813 rs148563931 rs74751226 rs8068857 rs8069441 rs77397878
rs56192520 0.006 0.006 0.006 0.006 0.006 0.006
rs3764410 0.006 0.006 0.006 0.006 0.006 0.006
rs145984817 0.006 0.006 0.006 0.006 0.006 0.006
rs1807401 0.006 0.006 0.006 0.006 0.006 0.006
rs1807402 0.006 0.006 0.006 0.006 0.006 0.006
rs35350506 0.006 0.006 0.006 0.006 0.006 0.006
rs75339756 rs4608391 rs79569548 rs4275914 rs11870422 rs8075751
rs56192520 0.006 0.006 0.006 0.044 0.007 0.004
rs3764410 0.006 0.006 0.006 0.042 0.005 0.005
rs145984817 0.006 0.006 0.006 0.047 0.002 0.015
rs1807401 0.006 0.006 0.006 0.047 0.002 0.015
rs1807402 0.006 0.006 0.006 0.047 0.002 0.015
rs35350506 0.006 0.006 0.006 0.047 0.002 0.015
rs11658904 rs138437542 rs80344434 rs7222311 rs7221842 rs7223686
rs56192520 0.003 0.004 0.004 0.033 0.009 0.000
rs3764410 0.004 0.004 0.004 0.031 0.007 0.000
rs145984817 0.010 0.004 0.004 0.035 0.011 0.005
rs1807401 0.010 0.004 0.004 0.035 0.011 0.005
rs1807402 0.010 0.004 0.004 0.035 0.011 0.005
rs35350506 0.010 0.004 0.004 0.035 0.011 0.005
rs78013597 rs74965036 rs78063986 rs118106233 rs117345712
rs56192520 0.004 0.004 0.004 0.004 0.005
rs3764410 0.004 0.004 0.004 0.004 0.006
rs145984817 0.004 0.004 0.004 0.004 0.005
rs1807401 0.004 0.004 0.004 0.004 0.005
rs1807402 0.004 0.004 0.004 0.004 0.005
rs35350506 0.004 0.004 0.004 0.004 0.005
rs113004656 rs9898995 rs4985718 rs9893911 rs79110942 rs7208929
rs56192520 0.004 0.033 0.033 0.023 0.004 0.023
rs3764410 0.004 0.031 0.031 0.021 0.004 0.021
rs145984817 0.004 0.035 0.035 0.025 0.004 0.025
rs1807401 0.004 0.035 0.035 0.025 0.004 0.025
rs1807402 0.004 0.035 0.035 0.025 0.004 0.025
rs35350506 0.004 0.035 0.035 0.025 0.004 0.025
rs12601453 rs4078062 rs75129280 rs76664572 rs78961289 rs146364798
rs56192520 0.004 0.001 0.004 0.004 0.004 0.004
rs3764410 0.004 0.002 0.004 0.004 0.004 0.004
rs145984817 0.004 0.001 0.004 0.004 0.004 0.004
rs1807401 0.004 0.001 0.004 0.004 0.004 0.004
rs1807402 0.004 0.001 0.004 0.004 0.004 0.004
rs35350506 0.004 0.001 0.004 0.004 0.004 0.004
rs76715413 rs4078534 rs79457460 rs74369938 rs76423171 rs74668400
rs56192520 0 0.004 0.004 0.002 0.004 0.004
rs3764410 0 0.004 0.004 0.001 0.004 0.004
rs145984817 0 0.004 0.004 0.005 0.004 0.004
rs1807401 0 0.004 0.004 0.005 0.004 0.004
rs1807402 0 0.004 0.004 0.005 0.004 0.004
rs35350506 0 0.004 0.004 0.005 0.004 0.004
rs75146120 rs1135237 rs9914671 rs117759512 rs4985696 rs16961340
rs56192520 0.004 0.003 0.009 0.004 0.009 0.004
rs3764410 0.004 0.003 0.007 0.004 0.007 0.004
rs145984817 0.004 0.003 0.011 0.004 0.011 0.004
rs1807401 0.004 0.003 0.011 0.004 0.011 0.004
rs1807402 0.004 0.003 0.011 0.004 0.011 0.004
rs35350506 0.004 0.003 0.011 0.004 0.011 0.004
rs17794159 rs4247118 rs78572469 rs12601193 rs2349646 rs2090018
rs56192520 0.001 0.033 0.002 0.004 0.020 0.033
rs3764410 0.002 0.031 0.001 0.004 0.019 0.031
rs145984817 0.001 0.035 0.005 0.004 0.022 0.035
rs1807401 0.001 0.035 0.005 0.004 0.022 0.035
rs1807402 0.001 0.035 0.005 0.004 0.022 0.035
rs35350506 0.001 0.035 0.005 0.004 0.022 0.035
rs12601424 rs4985701 rs8064550 rs2271521 rs2271520 rs11078374
rs56192520 0.004 0.033 0.033 0.004 0.033 0.014
rs3764410 0.004 0.031 0.031 0.004 0.031 0.012
rs145984817 0.004 0.035 0.035 0.004 0.035 0.016
rs1807401 0.004 0.035 0.035 0.004 0.035 0.016
rs1807402 0.004 0.035 0.035 0.004 0.035 0.016
rs35350506 0.004 0.035 0.035 0.004 0.035 0.016
rs4985702 rs1124961 rs11652674 rs3924340 rs112450164 rs7208973
rs56192520 0.033 0.003 0.002 0.001 0.004 0.033
rs3764410 0.031 0.003 0.001 0.002 0.004 0.031
rs145984817 0.035 0.003 0.005 0.001 0.004 0.035
rs1807401 0.035 0.003 0.005 0.001 0.004 0.035
rs1807402 0.035 0.003 0.005 0.001 0.004 0.035
rs35350506 0.035 0.003 0.005 0.001 0.004 0.035
rs9910857 rs78574480 rs8072184 rs12602196 rs6502563 rs3744135
rs56192520 0.006 0.004 0.014 0.004 0.033 0.004
rs3764410 0.005 0.004 0.012 0.004 0.031 0.004
rs145984817 0.002 0.004 0.016 0.004 0.035 0.004
rs1807401 0.002 0.004 0.016 0.004 0.035 0.004
rs1807402 0.002 0.004 0.016 0.004 0.035 0.004
rs35350506 0.002 0.004 0.016 0.004 0.035 0.004
rs148779543 rs77689691 rs41319048 rs117340532 rs78647096 rs77712968
rs56192520 0 0.004 0.004 0.002 0.004 0.004
rs3764410 0 0.004 0.004 0.001 0.004 0.004
rs145984817 0 0.004 0.004 0.005 0.004 0.004
rs1807401 0 0.004 0.004 0.005 0.004 0.004
rs1807402 0 0.004 0.004 0.005 0.004 0.004
rs35350506 0 0.004 0.004 0.005 0.004 0.004
rs16961396 rs80054920 rs7206981 rs4985740 rs3803762 rs77103270
rs56192520 0.004 0.004 0.033 0.023 0.004 0.002
rs3764410 0.004 0.004 0.031 0.021 0.004 0.001
rs145984817 0.004 0.004 0.035 0.025 0.004 0.005
rs1807401 0.004 0.004 0.035 0.025 0.004 0.005
rs1807402 0.004 0.004 0.035 0.025 0.004 0.005
rs35350506 0.004 0.004 0.035 0.025 0.004 0.005
rs7207485 rs77342773 rs3826304 rs3744126 rs7210879 rs7211576
rs56192520 0.029 0.004 0.004 0.004 0.023 0.006
rs3764410 0.027 0.004 0.004 0.004 0.021 0.005
rs145984817 0.031 0.004 0.004 0.004 0.025 0.002
rs1807401 0.031 0.004 0.004 0.004 0.025 0.002
rs1807402 0.031 0.004 0.004 0.004 0.025 0.002
rs35350506 0.031 0.004 0.004 0.004 0.025 0.002
rs117967362 rs75978745 rs6502564 rs9894565 rs36079048 rs8076621
rs56192520 0.004 0.004 0.007 0.017 0 0.004
rs3764410 0.004 0.004 0.005 0.015 0 0.004
rs145984817 0.004 0.004 0.009 0.019 0 0.004
rs1807401 0.004 0.004 0.009 0.019 0 0.004
rs1807402 0.004 0.004 0.009 0.019 0 0.004
rs35350506 0.004 0.004 0.009 0.019 0 0.004
rs7218795 rs3803761 rs12602675 rs7208065 rs4985705 rs8080386
rs56192520 0.026 0.032 0 0.018 0.014 0.003
rs3764410 0.024 0.029 0 0.015 0.011 0.002
rs145984817 0.028 0.034 0 0.021 0.016 0.004
rs1807401 0.028 0.034 0 0.021 0.016 0.004
rs1807402 0.028 0.034 0 0.021 0.016 0.004
rs35350506 0.028 0.034 0 0.021 0.016 0.004
rs8065832 rs2018781 rs1736221 rs1736220 rs1736217 rs1708620
rs56192520 0.008 0.039 0.003 0.003 0.021 0.009
rs3764410 0.006 0.037 0.002 0.002 0.019 0.007
rs145984817 0.010 0.042 0.004 0.004 0.024 0.011
rs1807401 0.010 0.042 0.004 0.004 0.024 0.011
rs1807402 0.010 0.042 0.004 0.004 0.024 0.011
rs35350506 0.010 0.042 0.004 0.004 0.024 0.011
rs1708619 rs1736216 rs76319098 rs1736215 rs1736214 rs1708617
rs56192520 0.009 0.024 0.017 0.012 0.019 0.029
rs3764410 0.007 0.021 0.016 0.009 0.016 0.026
rs145984817 0.011 0.026 0.018 0.014 0.022 0.031
rs1807401 0.011 0.026 0.018 0.014 0.022 0.031
rs1807402 0.011 0.026 0.018 0.014 0.022 0.031
rs35350506 0.011 0.026 0.018 0.014 0.022 0.031
rs12602831 rs12602871 rs1736213 rs1736212 rs76045368 rs34518797
rs56192520 0.000 0.000 0.015 0.029 0.001 0.001
rs3764410 0.001 0.001 0.013 0.026 0.001 0.001
rs145984817 0.000 0.000 0.018 0.031 0.000 0.000
rs1807401 0.000 0.000 0.018 0.031 0.000 0.000
rs1807402 0.000 0.000 0.018 0.031 0.000 0.000
rs35350506 0.000 0.000 0.018 0.031 0.000 0.000
rs11078378 rs8079562 rs8065774 rs8066090 rs41337846 rs1736209
rs56192520 0.043 0.001 0.001 0.029 0.000 0.029
rs3764410 0.041 0.001 0.001 0.026 0.001 0.026
rs145984817 0.046 0.000 0.000 0.031 0.000 0.031
rs1807401 0.046 0.000 0.000 0.031 0.000 0.031
rs1807402 0.046 0.000 0.000 0.031 0.000 0.031
rs35350506 0.046 0.000 0.000 0.031 0.000 0.031
rs1736208 rs12949822 rs76246042 rs12600635 rs55689224 rs1736207
rs56192520 0.043 0.043 0.000 0.000 0.000 0.015
rs3764410 0.041 0.041 0.001 0.001 0.001 0.013
rs145984817 0.046 0.046 0.000 0.000 0.000 0.018
rs1807401 0.046 0.046 0.000 0.000 0.000 0.018
rs1807402 0.046 0.046 0.000 0.000 0.000 0.018
rs35350506 0.046 0.046 0.000 0.000 0.000 0.018
rs1708626 rs1736206 rs9896078 rs16961474 rs1708627 rs1736205
rs56192520 0.015 0.015 0.001 0.001 0.017 0.021
rs3764410 0.013 0.013 0.001 0.001 0.014 0.019
rs145984817 0.018 0.018 0.000 0.001 0.020 0.024
rs1807401 0.018 0.018 0.000 0.001 0.020 0.024
rs1807402 0.018 0.018 0.000 0.001 0.020 0.024
rs35350506 0.018 0.018 0.000 0.001 0.020 0.024
rs1708628 rs7220577 rs2294155 rs1736204 rs1736203 rs1736202
rs56192520 0.011 0.011 0.000 0.021 0.014 0.014
rs3764410 0.009 0.009 0.000 0.019 0.011 0.011
rs145984817 0.013 0.013 0.001 0.024 0.016 0.016
rs1807401 0.013 0.013 0.001 0.024 0.016 0.016
rs1807402 0.013 0.013 0.001 0.024 0.016 0.016
rs35350506 0.013 0.013 0.001 0.024 0.016 0.016
rs12937908 rs1736200 rs1708623 rs1708624 rs9894884 rs9901894
rs56192520 0.009 0.009 0.008 0.007 0.009 0.009
rs3764410 0.007 0.007 0.006 0.005 0.007 0.007
rs145984817 0.011 0.011 0.010 0.008 0.011 0.011
rs1807401 0.011 0.011 0.010 0.008 0.011 0.011
rs1807402 0.011 0.011 0.010 0.008 0.011 0.011
rs35350506 0.011 0.011 0.010 0.008 0.011 0.011
rs9903294 rs2472689 rs1630656 rs111478970 rs3182911 rs7219012
rs56192520 0.008 0.011 0.007 0.007 0.008 0.000
rs3764410 0.006 0.009 0.005 0.005 0.006 0.000
rs145984817 0.010 0.013 0.008 0.008 0.010 0.001
rs1807401 0.010 0.013 0.008 0.008 0.010 0.001
rs1807402 0.010 0.013 0.008 0.008 0.010 0.001
rs35350506 0.010 0.013 0.008 0.008 0.010 0.001
rs9890657 rs12453455 rs12947291 rs150267386 rs16961493 rs11652745
rs56192520 0.009 0.007 0.008 0.013 0.000 0.009
rs3764410 0.007 0.005 0.006 0.012 0.000 0.007
rs145984817 0.011 0.008 0.010 0.014 0.001 0.011
rs1807401 0.011 0.008 0.010 0.014 0.001 0.011
rs1807402 0.011 0.008 0.010 0.014 0.001 0.011
rs35350506 0.011 0.008 0.010 0.014 0.001 0.011
rs9907107 rs8070574 rs4985759 rs3866959 rs7219248 rs6502568
rs56192520 0.009 0.009 0.009 0.011 0.009 0.011
rs3764410 0.007 0.007 0.007 0.009 0.007 0.009
rs145984817 0.011 0.011 0.011 0.013 0.011 0.013
rs1807401 0.011 0.011 0.011 0.013 0.011 0.013
rs1807402 0.011 0.011 0.011 0.013 0.011 0.013
rs35350506 0.011 0.011 0.011 0.013 0.011 0.013
rs7220275 rs12450037 rs7225876 rs9892352 rs4985760 rs6502569
rs56192520 0.009 0.008 0.007 0.011 0.011 0.011
rs3764410 0.007 0.006 0.005 0.009 0.009 0.009
rs145984817 0.011 0.010 0.008 0.013 0.013 0.013
rs1807401 0.011 0.010 0.008 0.013 0.013 0.013
rs1807402 0.011 0.010 0.008 0.013 0.013 0.013
rs35350506 0.011 0.010 0.008 0.013 0.013 0.013
rs1029830 rs2012954 rs1029832 rs2270180 rs8072402 rs7221553
rs56192520 0.009 0.011 0.008 0.000 0.009 0.011
rs3764410 0.007 0.009 0.006 0.000 0.007 0.009
rs145984817 0.011 0.013 0.010 0.001 0.011 0.013
rs1807401 0.011 0.013 0.010 0.001 0.011 0.013
rs1807402 0.011 0.013 0.010 0.001 0.011 0.013
rs35350506 0.011 0.013 0.010 0.001 0.011 0.013
rs145597919 rs150772017 rs2041393 rs6502578 rs11078382 rs9912109
rs56192520 0.013 0.013 0.005 0.005 0 0.005
rs3764410 0.012 0.012 0.004 0.004 0 0.004
rs145984817 0.014 0.014 0.006 0.006 0 0.006
rs1807401 0.014 0.014 0.006 0.006 0 0.006
rs1807402 0.014 0.014 0.006 0.006 0 0.006
rs35350506 0.014 0.014 0.006 0.006 0 0.006
rs12601631 rs11869054 rs11869079 rs9912599 rs7220057 rs9896970
rs56192520 0 0 0 0 0 0
rs3764410 0 0 0 0 0 0
rs145984817 0 0 0 0 0 0
rs1807401 0 0 0 0 0 0
rs1807402 0 0 0 0 0 0
rs35350506 0 0 0 0 0 0
rs34121330 rs34668117 rs67773570 rs242252 rs955893 rs28583584
rs56192520 0.000 0.000 0 0.002 0.001 0.013
rs3764410 0.001 0.001 0 0.003 0.001 0.005
rs145984817 0.000 0.000 0 0.002 0.001 0.004
rs1807401 0.000 0.000 0 0.002 0.001 0.004
rs1807402 0.000 0.000 0 0.002 0.001 0.004
rs35350506 0.000 0.000 0 0.002 0.001 0.004
rs9944423 rs7217764 rs11651957 rs73978990 rs8071007 rs56044345
rs56192520 0.013 0.011 0.011 0.011 0.011 0.011
rs3764410 0.005 0.004 0.004 0.004 0.004 0.004
rs145984817 0.004 0.003 0.003 0.003 0.003 0.003
rs1807401 0.004 0.003 0.003 0.003 0.003 0.003
rs1807402 0.004 0.003 0.003 0.003 0.003 0.003
rs35350506 0.004 0.003 0.003 0.003 0.003 0.003
rs17804843
rs56192520 0
rs3764410 0
rs145984817 0
rs1807401 0
rs1807402 0
rs35350506 0
On Thu, Nov 14, 2019 at 2:59 PM Abby Spurdle <spurdle.a at gmail.com> wrote:
That's assuming your data was returned by head().
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.