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I have a distance matrix in this form, "_M" being the Mock genes and "_W" being the Wild_type genes. Now the distance matrix shows the distance between each and every gene (Even between mock genes) 

                 ENSG00000186340_M ENSG00000198176_M ENSG00000198742_M ENSG00000204217_M ENSG00000204490_M ENSG00000205250_M ENSG00000243709_M

ENSG00000005339_M   410.1728383          36.10055          83.36385          218.3354        410.770123          277.2033        410.770123
ENSG00000011465_M     0.7504737         409.56151         327.54562          191.2074          1.295231          132.5045          1.295231
ENSG00000039319_M    82.3574833         173.95419         256.39415          390.8659        582.936553          449.1682        582.936553

                  ENSG00000005339_W ENSG00000011465_W ENSG00000039319_W ENSG00000049323_W ENSG00000055130_W ENSG00000067560_W ENSG00000067900_W

ENSG00000005339_M    221.9562       409.7261224         117.04727        405.669658         193.75271          43.45059         179.09973
ENSG00000011465_M    559.6470         0.6048307         524.45115          3.819013         592.46519         431.00051         588.15446
ENSG00000039319_M    216.2970       581.8796708          57.54276        577.848465          97.77784         163.35507          36.63868

. What I want out of this distance matrix is the distance between all same genes but between Mock and Wild type. For example I want to extract just the sub-matrix. 

                  ENSG00000005339_W ENSG00000011465_W ENSG00000039319_W ENSG00000049323_W ENSG00000055130_W ENSG00000067560_W ENSG00000067900_W

ENSG00000005339_M    221.9562       409.7261224         117.04727        405.669658         193.75271          43.45059         179.09973
ENSG00000011465_M    559.6470         0.6048307         524.45115          3.819013         592.46519         431.00051         588.15446
ENSG00000039319_M    216.2970       581.8796708          57.54276        577.848465          97.77784         163.35507          36.63868

If you could see the gene name is same except for _M or _W at the end of the gene name.How can I extract the sub matrix from my distance matrix?

saamar rajput
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    Try `m[grep("M$",rownames(m)),grep("W$",colnames(m))]`, where `m` is your matrix. – nicola Sep 05 '16 at 12:21
  • If you see the second matrix (what i want) , you can see that the distance between mock gene ENSG00000005339_M to the wild_type gene ENSG00000005339_W is 221.9562 and then again from mock ENSG00000011465_M to wild ENSG00000011465_W is 0.6048307. the second gene distance has no significance but the first one does. @ZheyuanLi – saamar rajput Sep 05 '16 at 12:23

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