Dear all,
I try to do a matrix with this data but the warning massage had occur:
In matrix(x5, ncol = 6, byrow = T) :
data length [116] is not a sub-multiple or multiple of the number of rows [20]
I think the spacing problem cause this where double spacing and tabs are
everywhere!!
Secondly, I have a raw data (which i downloaded from the AutoGraph server)
where it has 2 data in one text file. How am i going to split it to two?? I
also need to make a command function so that i can do it for the other 38
similar types of data. Below show my command function and attach with is my
data. Kindly help me to solve these problems and thanks in advance.
fun<-function(filename)
{
x<-scan(file=filename,sep="\n",skip=12,what=character(0))
x1<-gsub("[][)(:\\,|\\-]","",x)
x2<-gsub("Telomere","NA",x1)
x3<-gsub("Decreasing order|Increasing order","",x2)
x4<-strsplit(x3,"\t")
x5<-unlist(x4)
y<-matrix(x5,ncol=6,byrow=T)
tc<-textConnection(apply(y,1,paste,collapse=" "))
w<-read.table(tc)
t<-as.data.frame(w)
attr(t,"names")=c("CS(O)","id","no.anchor","ref","loc.start","loc.end","CS(O).size","CS(O)ref.density","tested","loc.start","loc.end","breakp.start","breakp.end","den
of anchor")
return(t)
}
Cheers,
Anisah
---------------------------------
AutoGRAPH analysis in a flat-file format ( CS(O) locations, size,
breakpoints...):
----------------------------------------------------------------------------------
Reference Chromosome vs Dataset 3
---------------------------------
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 (27): cfa1: [ 3251712 - 12398289 ] 9146577 3 mmu18:
[ 24330828 - 90644456 ] ] 12398289, 13347136 [(2 )
CS 2 (19): cfa1: [ 13347136 - 18193820 ] 4846684 4 mmu1:
[ 113688560 - 106596368 ] ] 18193820, 19140840 [(3 )
CSO 3.1 (18): cfa1: [ 19140840 - 22178912 ] 3038072 6
mmu18: [ 66984412 - 63788168 ]- Decreasing order - ] 22178912, 23188292 [
(2 )
CSO 3.2 (4): cfa1: [ 23188292 - 24126920 ] 938628 4
mmu18: [ 69469888 - 70578512 ]- Increasing order - ] 24126920, 24190392 [(8
)
CS 4 (2): cfa1: [ 24190392 - 24265894 ] 75502 26 mmu18:
[ 70634048 - 70693560 ] ] 24265894, 24823786 [(7 )
CSO 5.1 (6): cfa1: [ 24823786 - 27113036 ] 2289250 3
mmu18: [ 71384360 - 73984760 ]- Increasing order - ] 27113036, 27418228 [
(13 )
CSO 5.2 (4): cfa1: [ 27418228 - 27578150 ] 159922 25
mmu18: [ 68532272 - 68058624 ]- Decreasing order - ] 27578150, 28055666 [(9
)
CS 6 (77): cfa1: [ 28055666 - 47327576 ] 19271910 4 mmu10:
[ 24284924 - 3134304 ] ] 47327576, 47940412 [(5 )
CSO 7.1 (15): cfa1: [ 47940412 - 51570228 ] 3629816 4
mmu17: [ 3283055 - 7577392 ]- Increasing order - ] 51570228, 51988448 [
(11 )
CSO 7.2 (16): cfa1: [ 51988448 - 57900888 ] 5912440 3
mmu17: [ 12850771 - 8003706 ]- Decreasing order - ] 57900888, 58482632 [
(11 )
CSO 7.3 (5): cfa1: [ 58482632 - 59714992 ] 1232360 4
mmu17: [ 13497139 - 14565909 ]- Increasing order - ] 59714992, 59864308 [(15
)
CSO 8.1 (8): cfa1: [ 59864308 - 60129744 ] 265436 30
mmu10: [ 33840808 - 33608556 ]- Decreasing order - ] 60129744, 60211840 [
(17 )
CSO 8.2 (21): cfa1: [ 60211840 - 65147456 ] 4935616 4
mmu10: [ 51273836 - 57483016 ]- Increasing order - ] 65147456, 65273344 [
(7 )
CSO 8.3 (21): cfa1: [ 65273344 - 72417520 ] 7144176 3
mmu10: [ 33201750 - 24858506 ]- Decreasing order - ] 72417520, 73256040 [(7
)
CS 9 (24): cfa1: [ 73256040 - 78879792 ] 5623752 4 mmu13:
[ 64301608 - 58167304 ] ] 78879792, 79088752 [(10 )
CS 10 (3): cfa1: [ 79088752 - 80616144 ] 1527392 2 mmu4:
[ 73484664 - 71603504 ] ] 80616144, 82195232 [(2 )
CS 11 (58): cfa1: [ 82195232 - 96913624 ] 14718392 4 mmu19:
[ 14515091 - 29676192 ] ] 96913624, 97163832 [(8 )
CS 12 (10): cfa1: [ 97163832 - 99948816 ] 2784984 4 mmu13:
[ 53424904 - 51664268 ] ] 99948816, 100087840 [(9 )
CSO 13.1 (4): cfa1: [ 100087840 - 100423328 ] 335488 12
mmu13: [ 51443540 - 51113392 ]- Decreasing order - ] 100423328, 101013264
[ (11 )
CSO 13.2 (17): cfa1: [ 101013264 - 102120080 ] 1106816 15
mmu13: [ 48589808 - 49694080 ]- Increasing order - ] 102271920, 102458192
[(25 )
CSO 14.1 (10): cfa1: [ 102458192 - 104863664 ] 2405472 4
mmu7: [ 11943329 - 5734576 ]- Decreasing order - ] 104863664, 105135376
[ (35 )
CSO 14.2 (37): cfa1: [ 105135376 - 106177648 ] 1042272 35
mmu7: [ 4683380 - 3212900 ]- Decreasing order - ] 106177648, 108473048
[(12 )
CSO 15.1 (89): cfa1: [ 108473048 - 110798176 ] 2325128 38
mmu7: [ 43298008 - 45792284 ]- Increasing order - ] 110798176, 110969024
[ (37 )
CSO 15.2 (94): cfa1: [ 110969024 - 114574736 ] 3605712 26
mmu7: [ 12159146 - 24376768 ]- Increasing order - ] 114574736, 114862176
[ (35 )
CSO 15.3 (18): cfa1: [ 114862176 - 115343008 ] 480832 37
mmu7: [ 25108812 - 24578816 ]- Decreasing order - ] 115343008, 115476528
[ (36 )
CSO 15.4 (137): cfa1: [ 115476528 - 124798800 ] 9322272
15 mmu7: [ 25328194 - 40672432 ]- Increasing order - ] 124798800,
Telomere [(-NA-)
Reference Chromosome 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 (71): cfa1: [ 3251712 - 24265894 ] 21014182 3 hsa18:
[ 132170848 - 49934572 ] ] 24265894, 24823786 [(7 )
CSO 2.1 (6): cfa1: [ 24823786 - 27113036 ] 2289250 3
hsa18: [ 48121156 - 46579500 ]- Decreasing order - ] 27113036, 27418228 [
(13 )
CSO 2.2 (4): cfa1: [ 27418228 - 27578150 ] 159922 25
hsa18: [ 13872043 - 13208795 ]- Decreasing order - ] 27578150, 28055666 [(9
)
CSO 3.1 (113): cfa1: [ 28055666 - 59714992 ] 31659326 4 hsa6:
[ 132311008 - 169714432 ]- Increasing order - ] 59714992, 59864308 [ (15 )
CSO 3.2 (50): cfa1: [ 59864308 - 72417520 ] 12553212 4 hsa6:
[ 116707976 - 131508152 ]- Increasing order - ] 72417520, 73256040 [(7 )
CSO 4.1 (12): cfa1: [ 73256040 - 75192808 ] 1936768 6 hsa9:
[ 98441680 - 96360824 ]- Decreasing order - ] 75192808, 75336136 [ (6 )
CSO 4.2 (51): cfa1: [ 75336136 - 91881664 ] 16545528 3 hsa9:
[ 89301960 - 70341312 ]- Decreasing order - ] 91881664, 92281272 [ (5 )
CSO 4.3 (22): cfa1: [ 92281272 - 96913624 ] 4632352 5 hsa9:
[ 261625 - 5755076 ]- Increasing order - ] 96913624, 98067040 [ (5 )
CSO 4.4 (15): cfa1: [ 98067040 - 100692560 ] 2625520 6
hsa9: [ 93833248 - 89771184 ]- Decreasing order - ] 100692560, 101013264
[ (13 )
CSO 4.5 (17): cfa1: [ 101013264 - 102120080 ] 1106816 15
hsa9: [ 95832896 - 94012312 ]- Decreasing order - ] 102271920, 102458192
[(25 )
CS 5 (40): cfa1: [ 102458192 - 105936824 ] 3478632 11
hsa19: [ 63765096 - 59618416 ] ] 105936824, 106097392 [(35 )
CSO 6.1 (7): cfa1: [ 106097392 - 106177648 ] 80256 87
hsa19: [ 59386008 - 59289816 ]- Decreasing order - ] 106177648, 108260368 [
(11 )
CSO 6.2 (60): cfa1: [ 108260368 - 110263696 ] 2003328 30
hsa19: [ 56908176 - 54256216 ]- Decreasing order - ] 110263696, 110288752
[ (60 )
CSO 6.3 (71): cfa1: [ 110288752 - 112727048 ] 2438296 29
hsa19: [ 54163196 - 50959884 ]- Decreasing order - ] 112727048, 112775144
[(40 )
CS 7 (185): cfa1: [ 112775144 - 121690672 ] 8915528 21
hsa19: [ 50887772 - 38556448 ] ] 121690672, 121820640 [(16 )
CS 8 (20): cfa1: [ 121820640 - 124798800 ] 2978160 7
hsa19: [ 38391408 - 34709332 ] ] 124798800, Telomere [(-NA-)
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