Dear All,
I've successfully import my synteny data to R by using scan command. Below
show my results. My major problem with my data is how am i going to combine the
column names with the data( splt) where i have tried on cbind but a warning
message occur. I have realized that the splt data only have 5 column instead of
6. Please help me with this!!
I want my data to be a numerical data with a proper column and column names
and to replace CS with 1 and CSO with 0 and also to get remove all the
punctuations and the characters from the data.
Attach herewith is my original data. Your kindly help is highly appreciated
and thanks in advance.
Cheers,
Anisah
1)for col names
nms<-scan("C:/Users/user/Documents/cfa-1.txt",sep="\t",nlines=1,skip=10,what=character(0))
Read 6 items
> nms
[1] "CS(O) id (number of marker/anchor) "
[2] " Location(s) on reference "
[3] "CS(O) size"
[4] "CS(O) density on reference chromosome"
[5] "Location(s) on tested "
[6] "Breakpoints CS(O) locations (denstiy of marker/anchor)"
2) my data
x<-scan("C:/Users/user/Documents/cfa-1.txt",sep="\n",skip=12,what=character(0))
Read 21 items
> splt<-strsplit(x,"\t")
> splt
[[1]]
[1] "CS 1 (73): " " cfa1: [ 3251712 - 24126920 ] "
[3] " 20875208 " " 3 "
[5] " hsa18: [ 132170848 - 50139168 ] " "] 24126920, 24153560 [(8 ) "
[[2]]
[1] "CS 2 (3): " " cfa1: [ 24153560 - 24265894 ] "
[3] " 112334 " " 27 "
[5] " hsa18: [ 50105060 - 49934572 ] " "] 24265894, 24823786 [(7 ) "
[[3]]
[1] "CSO 3.1 (6): "
[2] " cfa1: [ 24823786 - 27113036 ] "
[3] " 2289250 "
[4] " 3 "
[5] " hsa18: [ 48121156 - 46579500 ]- Decreasing order - ] 27113036, 27418228 [
(13)"
[[4]]
[1] "CSO 3.2 (4): "
[2] " cfa1: [ 27418228 - 27578150 ] "
[3] " 159922 "
[4] " 25 "
[5] " hsa18: [ 13872043 - 13208795 ]- Decreasing order - ] 27578150, 28055666
[(9 ) "
[[5]]
[1] "CS 4 (4): " " cfa1: [ 28055666 - 28835230 ] "
[3] " 779564 " " 5 "
[5] " hsa6: [ 132311008 - 133132200 ] " "] 28835230, 29482792 [(7 ) "
[[6]]
[1] "CS 5 (46): " " cfa1: [ 29482792 - 40120672 ] "
[3] " 10637880 " " 4 "
[5] " hsa6: [ 133604208 - 146227152 ] " "] 40120672, 40539680 [(8 ) "
[[7]]
[1] "CS 6 (9): " " cfa1: [ 40539680 - 43339444 ] "
[3] " 2799764 " " 3 "
[5] " hsa6: [ 146390608 - 149867328 ] " "] 43339444, 43390788 [(13 ) "
[[8]]
[1] "CSO 7.1 (74): "
[2] " cfa1: [ 43390788 - 59714992 ] "
[3] " 16324204 "
[4] " 5 "
[5] " hsa6: [ 149929104 - 169714432 ]- Increasing order -] 59714992, 59864308 [
(15)"
[[9]]
[1] "CSO 7.2 (52): "
[2] " cfa1: [ 59864308 - 72417520 ] "
[3] " 12553212 "
[4] " 4 "
[5] " hsa6: [ 116707976 - 131508152 ]- Increasing order - "
[6] "] 72417520, 73256040 [(7 ) "
[[10]]
[1] "CSO 8.1 (12): "
[2] " cfa1: [ 73256040 - 75192808 ] "
[3] " 1936768 "
[4] " 6 "
[5] " hsa9: [ 98441680 - 96360824 ]- Decreasing order - "
[6] "] 75192808, 75272528 [ "
[7] " (6 )"
[[11]]
[1] "CSO 8.2 (56): "
[2] " cfa1: [ 75272528 - 91881664 ] "
[3] " 16609136 "
[4] " 3 "
[5] " hsa9: [ 89530256 - 70341312 ]- Decreasing order - "
[6] "] 91881664, 92281272 [ "
[7] " (5 )"
[[12]]
[1] "CSO 8.3 (22): "
[2] " cfa1: [ 92281272 - 96913624 ] "
[3] " 4632352 "
[4] " 5 "
[5] " hsa9: [ 261625 - 5755076 ]- Increasing order - "
[6] "] 96913624, 98067040 [ "
[7] " (5 )"
[[13]]
[1] "CSO 8.4 (15): "
[2] " cfa1: [ 98067040 - 100692560 ] 2625520 "
[3] " 6 "
[4] " hsa9: [ 93833248 - 89771184 ]- Decreasing order - ] 100692560, 101013264
[ "
[5] "(13 )"
[[14]]
[1] "CSO 8.5 (18): "
[2] " cfa1: [ 101013264 - 102120080 ] 1106816 "
[3] " 16 "
[4] " hsa9: [ 95832896 - 94012312 ]- Decreasing order -] 102271920,102458192
[(25 ) "
[[15]]
[1] "CS 9 (55): "
[2] " cfa1: [ 102458192 - 105936824 ] 3478632 "
[3] " 16 "
[4] " hsa19: [ 63765096 - 59618416 ] "
[5] "] 105936824, 106097392 [(35 ) "
[[16]]
[1] "CSO 10.1 (81): "
[2] " cfa1: [ 106097392 - 110263696 ] 4166304 "
[3] " 19 "
[4] " hsa19: [ 59386008 - 54256216 ]- Decreasing order - "
[5] "] 110263696,110288752 [ (60 )"
[[17]]
[1] "CSO 10.2 (18): "
[2] " cfa1: [ 110288752 - 110567608 ] 278856 "
[3] " 65 "
[4] " hsa19: [ 54163196 - 53814360 ]- Decreasing order - "
[5] "] 110567608,110575576 [ (50 )"
[[18]]
[1] "CSO 10.3 (60): "
[2] " cfa1: [ 110575576 - 112727048 ] 2151472 "
[3] " 28 "
[4] " hsa19: [ 53649284 - 50959884 ]- Decreasing order - "
[5] "] 112727048,112775144 [(40 ) "
[[19]]
[1] "CS 11 (173): "
[2] " cfa1: [ 112775144 - 119848336 ] 7073192 "
[3] " 24 "
[4] " hsa19: [ 50887772 - 40849556 ] "
[5] "] 119848336, 119880560 [(55 ) "
[[20]]
[1] "CS 12 (33): "
[2] " cfa1: [ 119880560 - 121690672 ] 1810112 "
[3] " 18 "
[4] " hsa19: [ 40824500 - 38556448 ] "
[5] "] 121690672, 121820640 [(16 ) "
[[21]]
[1] "CS 13 (22): "
[2] " cfa1: [ 121820640 - 124798800 ] 2978160 "
[3] " 7 "
[4] " hsa19: [ 38391408 - 34709332 ] "
[5] "] 124798800, Telomere [(-NA-) "
---------------------------------
Listing breakpoints, Conserved Segments and Conserved Segments Ordered
locations :
----------------------------------------------------------------------------------
Reference Chromosome (1) vs Dataset 2
---------------------------------
CS(O) id (number of marker/anchor) Location(s) on reference CS(O)
size CS(O) density on reference chromosome Location(s) on tested
Breakpoints CS(O) locations (denstiy of marker/anchor)
CS 1 (73): cfa1: [ 3251712 - 24126920 ] 20875208 3 hsa18:
[ 132170848 - 50139168 ] ] 24126920, 24153560 [(8 )
CS 2 (3): cfa1: [ 24153560 - 24265894 ] 112334 27 hsa18:
[ 50105060 - 49934572 ] ] 24265894, 24823786 [(7 )
CSO 3.1 (6): cfa1: [ 24823786 - 27113036 ] 2289250 3 hsa18:
[ 48121156 - 46579500 ]- Decreasing order - ] 27113036, 27418228 [ (13)
CSO 3.2 (4): cfa1: [ 27418228 - 27578150 ] 159922 25 hsa18:
[ 13872043 - 13208795 ]- Decreasing order - ] 27578150, 28055666 [(9 )
CS 4 (4): cfa1: [ 28055666 - 28835230 ] 779564 5 hsa6:
[ 132311008 - 133132200 ] ] 28835230, 29482792 [(7 )
CS 5 (46): cfa1: [ 29482792 - 40120672 ] 10637880 4 hsa6:
[ 133604208 - 146227152 ] ] 40120672, 40539680 [(8 )
CS 6 (9): cfa1: [ 40539680 - 43339444 ] 2799764 3 hsa6:
[ 146390608 - 149867328 ] ] 43339444, 43390788 [(13 )
CSO 7.1 (74): cfa1: [ 43390788 - 59714992 ] 16324204 5 hsa6:
[ 149929104 - 169714432 ]- Increasing order -] 59714992, 59864308 [ (15)
CSO 7.2 (52): cfa1: [ 59864308 - 72417520 ] 12553212 4 hsa6:
[ 116707976 - 131508152 ]- Increasing order - ] 72417520, 73256040 [(7 )
CSO 8.1 (12): cfa1: [ 73256040 - 75192808 ] 1936768 6 hsa9:
[ 98441680 - 96360824 ]- Decreasing order - ] 75192808, 75272528 [ (6 )
CSO 8.2 (56): cfa1: [ 75272528 - 91881664 ] 16609136 3 hsa9:
[ 89530256 - 70341312 ]- Decreasing order - ] 91881664, 92281272 [ (5 )
CSO 8.3 (22): cfa1: [ 92281272 - 96913624 ] 4632352 5 hsa9:
[ 261625 - 5755076 ]- Increasing order - ] 96913624, 98067040 [ (5 )
CSO 8.4 (15): cfa1: [ 98067040 - 100692560 ] 2625520 6 hsa9:
[ 93833248 - 89771184 ]- Decreasing order - ] 100692560, 101013264 [ (13 )
CSO 8.5 (18): cfa1: [ 101013264 - 102120080 ] 1106816 16 hsa9:
[ 95832896 - 94012312 ]- Decreasing order -] 102271920,102458192 [(25 )
CS 9 (55): cfa1: [ 102458192 - 105936824 ] 3478632 16 hsa19:
[ 63765096 - 59618416 ] ] 105936824, 106097392 [(35 )
CSO 10.1 (81): cfa1: [ 106097392 - 110263696 ] 4166304 19 hsa19:
[ 59386008 - 54256216 ]- Decreasing order - ] 110263696,110288752 [ (60 )
CSO 10.2 (18): cfa1: [ 110288752 - 110567608 ] 278856 65 hsa19:
[ 54163196 - 53814360 ]- Decreasing order - ] 110567608,110575576 [ (50 )
CSO 10.3 (60): cfa1: [ 110575576 - 112727048 ] 2151472 28 hsa19:
[ 53649284 - 50959884 ]- Decreasing order - ] 112727048,112775144 [(40 )
CS 11 (173): cfa1: [ 112775144 - 119848336 ] 7073192 24 hsa19:
[ 50887772 - 40849556 ] ] 119848336, 119880560 [(55 )
CS 12 (33): cfa1: [ 119880560 - 121690672 ] 1810112 18 hsa19:
[ 40824500 - 38556448 ] ] 121690672, 121820640 [(16 )
CS 13 (22): cfa1: [ 121820640 - 124798800 ] 2978160 7 hsa19:
[ 38391408 - 34709332 ] ] 124798800, Telomere [(-NA-)
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