Question

Gaia results including negative widths

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Talip Zengin ▴ 10

@talip-zengin-14290

Last seen 2.9 years ago

Mugla, Turkiye

Hello,
I perform CNV analysis by using TCGA data against hg38 and gaia package. After gaia results, at the annotation part, GenomicRanges gives error because of negative widths as below:

sCNV_GR <- makeGRangesFromDataFrame(sCNV,keep.extra.columns = TRUE)
Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") :
  solving row 2: negative widths are not allowed

When I checked gaia results, there are negative widths as below:

Chromosome   Aberration   Region Start [bp]   Region End [bp]   Region Size [bp]     q-value          score
1                       0                  152583408            152614064           30657                     0.023176209   1.634958
3                       0                  193155915          52994359           -140161555           0.027163423   1.566016
3                       1                  162795304            58872140             -103923163            0.002889900   2.539117
18             0                  ~~69085217~~              28616148             -40469068              0.039531082   1.403061
21                     0                  46570289            10756731           -35813557              0.002889900   2.539117

When I checked the genomic locations of patients, all they have positive widths as below:

Sample.Name Chromosome Start End Num.of.Markers Aberration

TCGA-L9-A443-01A-12D-A24C-01     3                      184250199    193155915   6251                      0
TCGA-49-AAR4-11A-11D-A412-01    3                       52994359    53005247       39                          0
TCGA-64-5781-01A-01D-1624-01     3                       52994359    53005473       42                          0
TCGA-44-2656-01A-02D-A273-01     3                       52994359    53005100       37                          0
TCGA-49-4494-11A-01D-1204-01     3                       52994359    53005100       37                          0

TCGA-49-AARR-11A-11D-A412-01    21         46570095     46570289       3                          0
TCGA-L9-A443-01A-12D-A24C-01    21                     10512696     10756731       65                         0
TCGA-73-A9RS-10A-01D-A412-01    21                     10568901     10756731       34                         1
TCGA-55-A491-10A-01D-A24E-01    21                     10336543     10756731       112                       0

Gaia results show the end position of patient as start and the start position of patients as end in results. Another one gives the range of end positions of patients. The interesting one is the position on chromosome 18 that is not exist in cnvMatrix.

When I checked the location of markers (in snp6.na35.liftoverhg38.txt file), SNP_A-1840697 (184250199) is on - strand, CN_994739 (193155915), SNP_A-2136119 (52994359) and others (53005247, 53005473, 53005100) are on + strand. For the second group of patients only marker CN_893664 (46570289) is on + strand and the others (46570095, 10756731, 10512696, 10568901, 10336543) are on - strand. But I did not give strand information in markersMatrix.

I am very confused. And I could not understand how gaia works. How can I fix this problem (negative widths)? Should I swap the locations? But I wonder to miss the important genes while annotation.

Thanks in advance for any help.

gaia genomicranges iranges • 1.5k views

ADD COMMENT • link updated 6.3 years ago by Sandro Morganella ▴ 40 • written 6.3 years ago by Talip Zengin ▴ 10

score 3 · Accepted Answer · 2018-08-09

Hi Talip, The probe positions must be sorted by their genomic position. Sorting the probes will fix your problem. Best, Sandro On Thu, Aug 9, 2018 at 3:23 PM, Talip Zengin [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Talip Zengin <https: support.bioconductor.org="" u="" 14290=""/> wrote Question: > Gaia results including negative widths > <https: support.bioconductor.org="" p="" 111894=""/>: > > Hello, > I perform CNV analysis by using TCGA data against hg38 and gaia package. > After gaia results, at the annotation part, GenomicRanges gives error > because of negative widths as below: > > sCNV_GR <- makeGRangesFromDataFrame(sCNV,keep.extra.columns = TRUE) > Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : > solving row 2: negative widths are not allowed > > When I checked gaia results, there are negative widths as below: > > Chromosome Aberration Region Start [bp] Region End [bp] Region > Size [bp] q-value score > 1 0 152583408 > 152614064 30657 0.023176209 1.634958 > 3 0 *193155915* > *52994359 * -140161555 0.027163423 1.566016 > 3 1 162795304 > 58872140 -103923163 0.002889900 2.539117 > 18 0 69085217 > 28616148 -40469068 0.039531082 1.403061 > 21 0 *46570289* *10756731* > -35813557 0.002889900 2.539117 > > When I checked the genomic locations of patients, all they have positive > widths as below: > > Sample.Name Chromosome > Start End Num.of.Markers Aberration > > TCGA-L9-A443-01A-12D-A24C-01 3 184250199 > *193155915* 6251 0 > TCGA-49-AAR4-11A-11D-A412-01 3 * 52994359* > 53005247 39 0 > TCGA-64-5781-01A-01D-1624-01 3 *52994359* > 53005473 42 0 > TCGA-44-2656-01A-02D-A273-01 3 *52994359* > 53005100 37 0 > TCGA-49-4494-11A-01D-1204-01 3 *52994359* > 53005100 37 0 > > TCGA-49-AARR-11A-11D-A412-01 21 46570095 > *46570289* 3 0 > TCGA-L9-A443-01A-12D-A24C-01 21 10512696 > *10756731* 65 0 > TCGA-73-A9RS-10A-01D-A412-01 21 10568901 > *10756731* 34 1 > TCGA-55-A491-10A-01D-A24E-01 21 10336543 > *10756731* 112 0 > > Gaia results show the end position of patient as start and the start > position of patients as end in results. Another one gives the range of end > positions of patients. The interesting one is the position on chromosome 18 > that is not exist in cnvMatrix. > > When I checked the location of markers (in snp6.na35.liftoverhg38.txt > file), SNP_A-1840697 (*184250199*) is on - strand, CN_994739 (*193155915*), > SNP_A-2136119 (*52994359*) and others (53005247, 53005473, 53005100) are > on + strand. For the second group of patients only marker CN_893664 ( > *46570289*) is on + strand and the others (46570095, *10756731, *10512696, > 10568901, 10336543) are on - strand. *But I did not give strand > information in markersMatrix.* > > I am very confused. And I could not understand how gaia works. How can I > fix this problem (negative widths)? Should I swap the locations? But I > wonder to miss the important genes while annotation. > > Thanks in advance for any help. > > ------------------------------ > > Post tags: gaia, genomicranges, iranges > > You may reply via email or visit https://support.bioconductor. > org/p/111894/ > -- - Sandro Morganella -