Question

DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"

1

Entering edit mode

jose.ramirez1 ▴ 10

@a3f49c6c

Last seen 12 months ago

Spain

Hi,

I am trying to use DMR.Plot but depending on the DMR I get the correct output or an error. I am using always the same set of beta values and the first part of the plot works but the last (the group means) does not. I want this last part to be divided into three groups, if I group into two instead some other DMR work, but not all. In some cases if I add to the beta values + 0.0000001 or - 0.0000001, it seems to work, but again, it depends on the region.

The error is the following one: "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"

It is obtained when calling plotTracks() from Gviz within the DMR.PLot function, but I do not have NAs, 0s or 1s in the beta values. How can I solve this?

Thanks,

DMRcate Gviz • 826 views

ADD COMMENT • link updated 7 hours ago by russ.bainer ▴ 10 • written 13 months ago by jose.ramirez1 ▴ 10

0

Entering edit mode

Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something.

Notably the same code works on other input data vectors, which also ultimately consist of numeric values between 0 and 4.

> temp
DataTrack 'BE4max'
| genome: ENST00000260526
| active chromosome: ENST00000260526
| positions: 1269
| samples:1
| strand: * 
> str(temp)
Formal class 'DataTrack' [package "Gviz"] with 8 slots
  ..@ data      : num [1, 1:1269] 0 0 0 0 0 0 0 0 1 0 ...
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : chr "V1"
  .. .. ..$ : NULL
  ..@ strand    : chr "*"
  ..@ range     :Formal class 'GRanges' [package "GenomicRanges"] with 7 slots
  .. .. ..@ seqnames       :Formal class 'Rle' [package "S4Vectors"] with 4 slots
  .. .. .. .. ..@ values         : Factor w/ 1 level "ENST00000260526": 1
  .. .. .. .. ..@ lengths        : int 1269
  .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. ..@ metadata       : list()
  .. .. ..@ ranges         :Formal class 'IRanges' [package "IRanges"] with 6 slots
  .. .. .. .. ..@ start          : int [1:1269] 1 2 3 4 5 6 7 8 9 10 ...
  .. .. .. .. ..@ width          : int [1:1269] 2 2 2 2 2 2 2 2 2 2 ...
  .. .. .. .. ..@ NAMES          : NULL
  .. .. .. .. ..@ elementType    : chr "ANY"
  .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. ..@ metadata       : list()
  .. .. ..@ strand         :Formal class 'Rle' [package "S4Vectors"] with 4 slots
  .. .. .. .. ..@ values         : Factor w/ 3 levels "+","-","*": 3
  .. .. .. .. ..@ lengths        : int 1269
  .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. ..@ metadata       : list()
  .. .. ..@ seqinfo        :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots
  .. .. .. .. ..@ seqnames   : chr "ENST00000260526"
  .. .. .. .. ..@ seqlengths : int NA
  .. .. .. .. ..@ is_circular: logi NA
  .. .. .. .. ..@ genome     : chr "ENST00000260526"
  .. .. ..@ elementMetadata:Formal class 'DFrame' [package "S4Vectors"] with 6 slots
  .. .. .. .. ..@ rownames       : NULL
  .. .. .. .. ..@ nrows          : int 1269
  .. .. .. .. ..@ elementType    : chr "ANY"
  .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. ..@ metadata       : list()
  .. .. .. .. ..@ listData       : Named list()
  .. .. ..@ elementType    : chr "ANY"
  .. .. ..@ metadata       : list()
  ..@ chromosome: chr "ENST00000260526"
  ..@ genome    : Named chr "ENST00000260526"
  .. ..- attr(*, "names")= chr "ENST00000260526"
  ..@ dp        :Formal class 'DisplayPars' [package "Gviz"] with 1 slot
  .. .. ..@ pars:List of 110
  .. .. .. ..$ aggregateGroups  : logi FALSE
  .. .. .. ..$ aggregation      : chr "mean"
  .. .. .. ..$ missingAsZero    : logi TRUE
  .. .. .. ..$ alpha.confint    : num 0.3
  .. .. .. ..$ amount           : NULL
  .. .. .. ..$ baseline         : NULL
  .. .. .. ..$ box.legend       : logi FALSE
  .. .. .. ..$ box.ratio        : num 1
  .. .. .. ..$ box.width        : NULL
  .. .. .. ..$ grid             : logi FALSE
  .. .. .. ..$ cex.legend       : num 0.8
  .. .. .. ..$ cex.sampleNames  : NULL
  .. .. .. ..$ cex              : num 0.7
  .. .. .. ..$ coef             : num 1.5
  .. .. .. ..$ col.baseline     : NULL
  .. .. .. ..$ col.confint      : logi NA
  .. .. .. ..$ col.boxplotFrame : chr "#808080"
  .. .. .. ..$ col.histogram    : chr "#808080"
  .. .. .. ..$ col.horizon      : logi NA
  .. .. .. ..$ col.mountain     : NULL
  .. .. .. ..$ col.sampleNames  : chr "white"
  .. .. .. ..$ col              : Named chr [1:7] "#0072B2" "#E69F00" "#009E73" "#D55E00" ...
  .. .. .. .. ..- attr(*, "names")= chr [1:7] "blue" "orange" "bluishgreen" "vermillion" ...
  .. .. .. ..$ collapse         : logi FALSE
  .. .. .. ..$ degree           : num 1
  .. .. .. ..$ do.out           : logi TRUE
  .. .. .. ..$ evaluation       : num 50
  .. .. .. ..$ factor           : num 0.5
  .. .. .. ..$ family           : chr "symmetric"
  .. .. .. ..$ fill.confint     : NULL
  .. .. .. ..$ fill.histogram   : NULL
  .. .. .. ..$ fill.horizon     : chr [1:6] "#B41414" "#E03231" "#F7A99C" "#9FC8DC" ...
  .. .. .. ..$ fill.mountain    : chr [1:2] "#CCFFFF" "#FFCCFF"
  .. .. .. ..$ fontface.legend  : NULL
  .. .. .. ..$ fontfamily.legend: NULL
  .. .. .. ..$ fontsize.legend  : NULL
  .. .. .. ..$ fontcolor.legend : chr "#808080"
  .. .. .. ..$ gradient         : chr [1:9] "#F7FBFF" "#DEEBF7" "#C6DBEF" "#9ECAE1" ...
  .. .. .. ..$ groups           : NULL
  .. .. .. ..$ horizon.origin   : num 0
  .. .. .. ..$ horizon.scale    : NULL
  .. .. .. ..$ jitter.x         : logi FALSE
  .. .. .. ..$ jitter.y         : logi FALSE
  .. .. .. ..$ levels.fos       : NULL
  .. .. .. ..$ legend           : logi TRUE
  .. .. .. ..$ lineheight.legend: NULL
  .. .. .. ..$ lty.baseline     : NULL
  .. .. .. ..$ lty.mountain     : NULL
  .. .. .. ..$ lwd.baseline     : NULL
  .. .. .. ..$ lwd.mountain     : NULL
  .. .. .. ..$ min.distance     : num 0
  .. .. .. ..$ na.rm            : logi FALSE
  .. .. .. ..$ ncolor           : num 100
  .. .. .. ..$ notch.frac       : num 0.5
  .. .. .. ..$ notch            : logi FALSE
  .. .. .. ..$ pch              : num 20
  .. .. .. ..$ separator        : num 0
  .. .. .. ..$ showColorBar     : logi TRUE
  .. .. .. ..$ showSampleNames  : logi FALSE
  .. .. .. ..$ size             : NULL
  .. .. .. ..$ span             : num 0.2
  .. .. .. ..$ stackedBars      : logi TRUE
  .. .. .. ..$ stats            :function (x, coef = 1.5, do.conf = TRUE, do.out = TRUE)  
  .. .. .. ..$ transformation   : NULL
  .. .. .. ..$ type             : chr [1:2] "h" "smooth"
  .. .. .. ..$ varwidth         : logi FALSE
  .. .. .. ..$ window           : NULL
  .. .. .. ..$ windowSize       : NULL
  .. .. .. ..$ ylim             : num [1:2] 0 4
  .. .. .. ..$ yTicksAt         : NULL
  .. .. .. ..$ .__appliedScheme : chr "default"
  .. .. .. ..$ alpha            : num 1
  .. .. .. ..$ alpha.title      : NULL
  .. .. .. ..$ background.panel : chr "white"
  .. .. .. ..$ background.title : chr "white"
  .. .. .. ..$ background.legend: chr "transparent"
  .. .. .. ..$ cex.axis         : NULL
  .. .. .. ..$ cex.title        : NULL
  .. .. .. ..$ col.axis         : chr "black"
  .. .. .. ..$ col.border.title : chr "white"
  .. .. .. ..$ col.frame        : chr "lightgray"
  .. .. .. ..$ col.grid         : chr "#808080"
  .. .. .. ..$ col.line         : NULL
  .. .. .. ..$ col.symbol       : NULL
  .. .. .. ..$ fontcolor.title  : chr "black"
  .. .. .. ..$ fill             : chr "lightgray"
  .. .. .. ..$ fontcolour       : chr "black"
  .. .. .. ..$ fontface.title   : num 2
  .. .. .. ..$ fontface         : num 1
  .. .. .. ..$ fontfamily.title : chr "sans"
  .. .. .. ..$ fontfamily       : chr "sans"
  .. .. .. ..$ fontsize         : num 12
  .. .. .. ..$ frame            : logi FALSE
  .. .. .. ..$ h                : num -1
  .. .. .. ..$ lineheight       : num 1
  .. .. .. ..$ lty.grid         : chr "solid"
  .. .. .. ..$ lty              : chr "solid"
  .. .. .. ..$ lwd.border.title : num 1
  .. .. .. ..$ lwd.title        : num 1
  .. .. .. ..$ lwd.grid         : num 1
  .. .. .. .. [list output truncated]
  ..@ name      : chr "BE4max"
  ..@ imageMap  : NULL
  ..$ columns: chr "score"
> plotTracks(temp)
Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE,  : 
  NA/NaN/Inf in foreign function call (arg 1)

ADD REPLY • link 7 hours ago russ.bainer ▴ 10