search

ShellyCoder / cellcall

inferring cell-cell communication from scRNA-seq of ligand-receptor
73 stars 20 forks source link

[bug] Error when creating object with Full-length df #14

Open PerrineLacour opened 2 years ago

PerrineLacour commented 2 years ago

Hi,

I tried to create an object using this command CreateNichConObject(data = reads_df, min.feature = 500, source = "fullLength", Org = "Mus musculus", names.delim = "M", names.field = 1) as shown in the tutorial.

I get this error message Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection In addition: Warning message: In readChar(con, 5L, useBytes = TRUE) : cannot open compressed file '', probable reason 'No such file or directory'

From what I could see, I think it comes from the counts2normalized_smartseq2 function when it tries to find the reference file for transcript length.

Do you know how I can fix that problem?

Best,

PerrineLacour commented 2 years ago

I tried overwriting the counts2normalized_smartse2 function and replacing the "cellwave" with "cellcall" in f.tmp <- system.file("extdata", "homo/transcriptmaxLength.Rdata", package="cellwave") and it works now.

Would it be possible to correct this problem?

Best,

ShellyCoder commented 2 years ago

Acctually your point is right, and i have revise this bug.

Thanks for your contributions !!

ShellyCoder commented 2 years ago

Your ability to catch code is admirable. Thank you again sincerely. Modification had be conducted.