check_dataset

Question

check_dataset

Closed this issue 2 years ago · 17 comments

Hi, I am trying to use my.res <- finemap.abf(dataset=D1,p1 = 1e-04),
now preparing the dateset, with

beta <- read.csv("C:/Users/xxxx/Desktop/beta.csv")
varbeta <- read.csv("C:/Users/xxxx/Desktop/varbeta.csv")
MAF <- read.csv("C:/Users/xxxx/Desktop/MAF.csv")
LD <- read.csv("C:/Users/xxxx/Desktop/LD.csv", row.names=1)

list_of_df <- list(beta,varbeta, "N" = 18000,"sdY" = 7,"type" = 'quant', MAF, LD)

names(list_of_df) <- c("beta","varbeta", "N" = 18000,"sdY" = 7,"type" = 'quant', "MAF", "LD")

check_dataset(list_of_df)

but having this error

Error in check_dataset(list_of_df) :
dataset : MAF should be a numeric, strictly >0 & <1

please advise, thanks.

Answer 1 · 2022-01-13T10:57:50.000Z

It says that some of your MAF values are either not numeric or are <=0 or are >= 1

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On Thu, 2022-01-13 at 02:55 -0800, MoMaz123 wrote: Hi, I am trying to use my.res <- finemap.abf(dataset=D1,p1 = 1e-04), now preparing the dateset, with beta <- read.csv("C:/Users/xxxx/Desktop/beta.csv") varbeta <- read.csv("C:/Users/xxxx/Desktop/varbeta.csv") MAF <- read.csv("C:/Users/xxxx/Desktop/MAF.csv") LD <- read.csv("C:/Users/xxxx/Desktop/LD.csv", row.names=1) list_of_df <- list(beta,varbeta, "N" = 18000,"sdY" = 7,"type" = 'quant', MAF, LD) names(list_of_df) <- c("beta","varbeta", "N" = 18000,"sdY" = 7,"type" = 'quant', "MAF", "LD") check_dataset(list_of_df) but having this error Error in check_dataset(list_of_df) : dataset : MAF should be a numeric, strictly >0 & <1 please advise, thanks. — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

Answer 2 · 2022-01-13T11:00:39.000Z

thanks,
that inst accurate because:

str(MAF)
'data.frame': 100 obs. of 1 variable:
$ EA_FREQ: num 0.000833 0.005551 0.002558 0.13733 0.000172 ...

right?

Answer 3 · 2022-01-13T11:14:33.000Z

MAF is supposed to be of class numeric, you have a data.frame

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On Thu, 2022-01-13 at 03:00 -0800, MoMaz123 wrote: thanks, that inst accurate because: > str(MAF) > 'data.frame': 100 obs. of 1 variable: > $ EA_FREQ: num 0.000833 0.005551 0.002558 0.13733 0.000172 ... right? — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you commented.Message ID: ***@***.***>

Answer 4 · 2022-01-13T11:19:29.000Z

Thanks indeed, now I have done:

MAF <- as.vector(MAF [,1])
str(MAF)

also changed the LD to matrix LD=data.matrix(LD)
now I am having this error,

check_dataset(list_of_df)
Error in check_dataset(list_of_df) :
dataset : lengths of inputs don't match:

Answer 5 · 2022-01-13T11:37:02.000Z

they all having the same length,

str(beta)
'data.frame': 100 obs. of 1 variable:
$ BETA: num 0.2305 -0.0634 0.012 0.0232 -0.5869 ...
str(varbeta)
'data.frame': 100 obs. of 1 variable:
$ SE: num 0.2474 0.0762 0.1222 0.0154 0.4904 ...
str(MAF)
num [1:100] 0.000833 0.005551 0.002558 0.13733 0.000172 ...
dim(LD)
[1] 100 100

Answer 6 · 2022-01-13T11:38:40.000Z

what is length(beta)?

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On Thu, 2022-01-13 at 03:37 -0800, MoMaz123 wrote: they all having the same length, > str(beta) > 'data.frame': 100 obs. of 1 variable: > $ BETA: num 0.2305 -0.0634 0.012 0.0232 -0.5869 ... > str(varbeta) > 'data.frame': 100 obs. of 1 variable: > $ SE: num 0.2474 0.0762 0.1222 0.0154 0.4904 ... > str(MAF) > num [1:100] 0.000833 0.005551 0.002558 0.13733 0.000172 ... > dim(LD) > [1] 100 100 — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you commented.Message ID: ***@***.***>

Answer 7 · 2022-01-13T11:40:36.000Z

length(beta)
[1] 1

Answer 8 · 2022-01-13T11:42:41.000Z

which is not the same as length(MAF). which is what the error says

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On Thu, 2022-01-13 at 03:40 -0800, MoMaz123 wrote: > length(beta) > [1] 1 — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you commented.Message ID: ***@***.***>

Answer 9 · 2022-01-13T11:43:35.000Z

Great thanks for pointing out,
how can I solve this issues, please.

Answer 10 · 2022-01-13T11:51:00.000Z

that solved, now another one is apear,

Error in check_dataset(dataset, "") : LD rownames != colnames

Answer 11 · 2022-01-13T11:52:41.000Z

beta <- read.csv("C:/Users/x/Desktop/beta.csv")
str(beta)
length(beta)

beta <- as.vector(beta [,1])

varbeta <- read.csv("C:/Users/x/Desktop/varbeta.csv")
str(varbeta)
length(varbeta)

varbeta <- as.vector(varbeta [,1])

MAF <- read.csv("C:/Users/x/Desktop/MAF.csv")

MAF <- as.vector(MAF [,1])
str(MAF)
class(MAF)
length(MAF)

LD <- read.csv("C:/Users/x/Desktop/LD.csv", row.names=1)
LD=data.matrix(LD)
dim(LD)

list_of_df <- list(beta,varbeta, "N" = 18000,"sdY" = 7,"type" = 'quant', MAF, LD)

names(list_of_df) <- c("beta","varbeta", "N" ,"sdY" , "type" , "MAF", "LD")

check_dataset(list_of_df)

having this error,

check_dataset(list_of_df)
Error in check_dataset(list_of_df) : LD rownames != colnames

Answer 12 · 2022-01-13T12:01:30.000Z

but they have the exact same name, Rows and Columns in the LD

Answer 13 · 2022-01-13T12:10:14.000Z

well the error says they don't. did you check? identical(rownames(LD),colnames(LD))

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On Thu, 2022-01-13 at 04:01 -0800, MoMaz123 wrote: but they have the exact same name, Rows and Columns in the LD — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you commented.Message ID: ***@***.***>

Answer 14 · 2022-01-13T13:15:21.000Z

Great thanks, it's done now.
just last question, the SNPs with the highest PP (SNP.PP) are the top hit?
Thanks, mo

Answer 15 · 2022-01-13T13:26:07.000Z

assuming H4 is true

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On Thu, 2022-01-13 at 05:15 -0800, MoMaz123 wrote: Great thanks, it's done now. just last question, the SNPs with the highest PP (SNP.PP) are the top hit? Thanks, mo — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you commented.Message ID: ***@***.***>

Answer 16 · 2022-01-13T13:33:19.000Z

sorry, what is H4?

Answer 17 · 2022-01-13T13:36:21.000Z

https://chr1swallace.github.io/coloc/articles/a03_enumeration.html

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On Thu, 2022-01-13 at 05:33 -0800, MoMaz123 wrote: sorry, what is H4? — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you commented.Message ID: ***@***.***>