mjnajafpanah
commented
3 months ago Dear SQUID user,
Thanks for your interest in our deconvolution tool.
SQUID is implemented for matching SC/Bulk samples (best case scenario) , however is also ability to deconvolve the unmatched bulk samples as well, if P is simply provided:
(1) having the (P.rds) file from your single cell study (P=P): P=readRDS("P.rds) SQUID <- function(B=B, scC=scC , scMeta=scMeta, pB=NULL, P=P, LeaveOneOut=FALSE)
(2) comment (#) the highlighted line in the code if you want to let SQUID generate the P for you (P=NULL).
SQUID <- function(B=B, scC=scC , scMeta=scMeta, pB=NULL, P=NULL, LeaveOneOut=FALSE)
Make proportional table (P), if not provided
if(is.null(P)){ P <- table(scMeta$sample.id, scMeta$cellType) %>% t() P <- P[,gtools::mixedsort(colnames(P))]
P <- P[,colnames(P) %in% colnames(B)] # generate P using matching sample IDs, comment this line if running unmated samples.
P <- apply(P, 2, function(x) x / sum(x))} else { P=P }
So, you just need to provide P using either of the above options.
Best, Mohammad
From: phoman14 @.> Sent: Friday, August 2, 2024 2:21 PM To: mjnajafpanah/SQUID @.> Cc: Subscribed @.***> Subject: [mjnajafpanah/SQUID] Error when Bulk Sample names do not Match Single Cell samples (Issue #1)
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I am trying to use a Single Cell dataset from from one project to deconvolute a Bulk RNAseq dataset from a different project. When i run Squid I am getting an error when SQUOD.R is trying to create the P table from the SingleCell data which forces a match between sample names in the Bulk Data. Line in Code referenced below.
https://github.com/mjnajafpanah/SQUID/blob/a6f01ad903a4f24d38d682bf4082d23404a54357/R/SQUID.R#L114https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_mjnajafpanah_SQUID_blob_a6f01ad903a4f24d38d682bf4082d23404a54357_R_SQUID.R-23L114&d=DwMCaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=4DhvbN7IEXgxPlg3Sc_Ok3yYJcjRdOyzoRnQ4SfoMTjDRRx-Ttmkm4px9ikg7uJL&m=sjAtxmfrLS-PjEUzz2kLaKD97dD9x2o0AamYUfxYxAFyWrzQYusMREA4z2oXmwWP&s=GhVVuCsJyISouxLpzzbOebrCmyphQfR7NsWzvWRLwMA&e=
Is there a reason why the sample names between two different datasets have to match? The single Cell and Bulk datasets are related but are not from the exact same sample. Can SQUID still be used for this type of analysis?
Thank you Philip Homan
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I am trying to use a Single Cell dataset from from one project to deconvolute a Bulk RNAseq dataset from a different project. When i run Squid I am getting an error when SQUOD.R is trying to create the P table from the SingleCell data which forces a match between sample names in the Bulk Data. Line in Code referenced below.
https://github.com/mjnajafpanah/SQUID/blob/a6f01ad903a4f24d38d682bf4082d23404a54357/R/SQUID.R#L114
Is there a reason why the sample names between two different datasets have to match? The single Cell and Bulk datasets are related but are not from the exact same sample. Can SQUID still be used for this type of analysis?
Thank you Philip Homan