check_dataset

[MoMaz123]

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.

[chr1swallace]

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

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: @.***>

[MoMaz123]

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?

[chr1swallace]

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

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: @.***>

[MoMaz123]

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:

[MoMaz123]

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

[chr1swallace]

what is length(beta)?

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: @.***>

[MoMaz123]

length(beta) [1] 1

[chr1swallace]

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

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: @.***>

[MoMaz123]

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

[MoMaz123]

that solved, now another one is apear,

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

[MoMaz123]

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

[MoMaz123]

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

[chr1swallace]

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

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: @.***>

[MoMaz123]

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

[chr1swallace]

assuming H4 is true

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: @.***>

[MoMaz123]

sorry, what is H4?

[chr1swallace]

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

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: @.***>