Amit
2010-Apr-30 14:14 UTC
[R] extracting pairs from correlation matrix and p-value matrix
Dear All, I am working on a large matrix of dimension 20000x700 say 'mat'. I have calculated pearson correlation for the rows of the matrix and their p-values using rcorr function in library Hmisc. Now I wish to filter out those pairs who's PCC value is above 0.8 cut off and p-value is less than 0.05.>library(Hmisc) >mat_cor=rcorr(t(mat),type="pearson") >head(mat_cor)aaeA_b3241_14 aaeB_b3240_15 aaeR_b3243_15 aaeX_b3242_12 aas_b2836_14 aat_b0885_14 abgA_b1338_14 abgB_b1337_15 abgR_b1339_15 abgT_b1336_15 aaeA_b3241_14 1.00 0.12 0.64 0.21 0.10 -0.68 -0.61 -0.62 -0.66 -0.67 aaeB_b3240_15 0.12 1.00 -0.57 0.26 -0.50 0.05 0.50 0.46 0.40 0.47 aaeR_b3243_15 0.64 -0.57 1.00 -0.02 0.45 -0.52 -0.93 -0.92 -0.91 -0.96 aaeX_b3242_12 0.21 0.26 -0.02 1.00 -0.45 -0.60 -0.20 -0.16 -0.22 -0.07 aas_b2836_14 0.10 -0.50 0.45 -0.45 1.00 -0.08 -0.53 -0.57 -0.52 -0.58 aat_b0885_14 -0.68 0.05 -0.52 -0.60 -0.08 1.00 0.63 0.61 0.64 0.59 abgA_b1338_14 -0.61 0.50 -0.93 -0.20 -0.53 0.63 1.00 0.99 0.99 0.98 abgB_b1337_15 -0.62 0.46 -0.92 -0.16 -0.57 0.61 0.99 1.00 1.00 0.99 abgR_b1339_15 -0.66 0.40 -0.91 -0.22 -0.52 0.64 0.99 1.00 1.00 0.98 abgT_b1336_15 -0.67 0.47 -0.96 -0.07 -0.58 0.59 0.98 0.99 0.98 1.00 n= 20000 P aaeA_b3241_14 aaeB_b3240_15 aaeR_b3243_15 aaeX_b3242_12 aas_b2836_14 aat_b0885_14 abgA_b1338_14 abgB_b1337_15 abgR_b1339_15 abgT_b1336_15 aaeA_b3241_14 0.7401 0.0457 0.5556 0.7774 0.0289 0.0629 0.0561 0.0371 0.0351 aaeB_b3240_15 0.7401 0.0868 0.4644 0.1435 0.8840 0.1375 0.1799 0.2522 0.1747 aaeR_b3243_15 0.0457 0.0868 0.9529 0.1915 0.1198 0.0000 0.0001 0.0002 0.0000 aaeX_b3242_12 0.5556 0.4644 0.9529 0.1905 0.0670 0.5813 0.6610 0.5441 0.8422 aas_b2836_14 0.7774 0.1435 0.1915 0.1905 0.8295 0.1167 0.0851 0.1224 0.0784 aat_b0885_14 0.0289 0.8840 0.1198 0.0670 0.8295 0.0521 0.0626 0.0449 0.0740 abgA_b1338_14 0.0629 0.1375 0.0000 0.5813 0.1167 0.0521 0.0000 0.0000 0.0000 abgB_b1337_15 0.0561 0.1799 0.0001 0.6610 0.0851 0.0626 0.0000 0.0000 0.0000 abgR_b1339_15 0.0371 0.2522 0.0002 0.5441 0.1224 0.0449 0.0000 0.0000 0.0000 abgT_b1336_15 0.0351 0.1747 0.0000 0.8422 0.0784 0.0740 0.0000 0.0000 0.0000 Now from mat_cor$r and mat_cor$P I wish to extract those pairs which satisfies the condition PCC>0.8 and p-value<0.05. But I am puzzled!! Please help. regards Amit