-
Notifications
You must be signed in to change notification settings - Fork 1
GSE131957 Ref matrices #33
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Merged
Merged
Changes from all commits
Commits
Show all changes
11 commits
Select commit
Hold shift + click to select a range
9af8c8b
Started extracting files from GSE131957
SidhantPuntambekar d7c51a9
Merge branch 'master' of https://github.com/rnabioco/scRNA-seq-Cell-R…
SidhantPuntambekar f7f6c8b
Loaded in csv file and metadata
SidhantPuntambekar 8325c0f
Fixed error with GSE124952
SidhantPuntambekar 4635555
Normalized data and added tumor R files
SidhantPuntambekar 6d12663
Did ccr7ko of GSE131957
SidhantPuntambekar c9d11b0
Added Beadneg but not going to use because normalized counts
SidhantPuntambekar f0531a3
Updated mouseAtlas.rds and reran meta-analysis
SidhantPuntambekar b0ada7e
Changed if_log back to false
SidhantPuntambekar 99d6277
Removed ADT ref matrices
SidhantPuntambekar b1dede1
Rewrote moumouseAtlas.rds
SidhantPuntambekar File filter
Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
There are no files selected for viewing
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,41 @@ | ||
| library(dplyr) | ||
| library(Seurat) | ||
| library(patchwork) | ||
| library(clustifyr) | ||
| library(tidyverse) | ||
| library(digest) | ||
| library(here) | ||
|
|
||
| proj_dir <- here() | ||
| GSE131957 <- file.path(proj_dir, "Reference-Matrix-Generation", "data", "GSE131957_Raw 2", "GSM3832743_beadneg_dc1_1.csv.gz") | ||
|
|
||
| mat_mouseLungLesions <- read.csv(GSE131957) | ||
| mat_mouseLungLesions <- mat_mouseLungLesions %>% | ||
| # as.data.frame() %>% | ||
| column_to_rownames('X') | ||
| # as.matrix() %>% | ||
| # t() | ||
| mat_mouseLungLesions[1:5, 1:5] | ||
|
|
||
| meta_mouseLungLesions <- read_csv("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131957/suppl/GSE131957_single_cell_metadata.csv.gz") | ||
| meta_mouseLungLesions <- meta_mouseLungLesions %>% column_to_rownames("X1") %>% t() %>% as.data.frame() | ||
| meta2 <- meta_mouseLungLesions[colnames(mat_mouseLungLesions),] | ||
| meta_mouseLungLesions | ||
| sum(colnames(mat_mouseLungLesions) %in% meta_mouseLungLesions$cluster) | ||
| ncol(mat_mouseLungLesions) | ||
|
|
||
| source("~/Reference-Matrix-Generation/R/utils/utils.r") | ||
| checkRawCounts(as.matrix(mat_mouseLungLesions)) | ||
|
|
||
| GSE131957WTNaiveNormalized <- NormalizeData(mat_mouseLungLesions) | ||
|
|
||
| new_ref_matrix <- average_clusters(mat = GSE131957WTNaiveNormalized, metadata = meta2, cluster_col = "cluster_annotation", if_log = FALSE) | ||
| new_ref_matrix_hashed <- average_clusters(mat = mat_mouseLungLesions, metadata = meta_mouseLungLesions, if_log = FALSE) | ||
| head(new_ref_matrix) | ||
| tail(new_ref_matrix) | ||
| newcols <- sapply(colnames(new_ref_matrix_hashed), digest, algo = "sha1") | ||
| colnames(new_ref_matrix_hashed) <- newcols | ||
| head(new_ref_matrix_hashed) | ||
| tail(new_ref_matrix_hashed) | ||
| saveRDS(new_ref_matrix_hashed, "GSE131957Hashed.rds") | ||
| saveRDS(new_ref_matrix, "GSE131957Beadneg1.rds") |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,41 @@ | ||
| library(dplyr) | ||
| library(Seurat) | ||
| library(patchwork) | ||
| library(clustifyr) | ||
| library(tidyverse) | ||
| library(digest) | ||
| library(here) | ||
|
|
||
| proj_dir <- here() | ||
| GSE131957 <- file.path(proj_dir, "Reference-Matrix-Generation", "data", "GSE131957_Raw 2", "GSM3832744_beadneg_dc1_2.csv.gz") | ||
|
|
||
| mat_mouseLungLesions <- read.csv(GSE131957) | ||
| mat_mouseLungLesions <- mat_mouseLungLesions %>% | ||
| # as.data.frame() %>% | ||
| column_to_rownames('X') | ||
| # as.matrix() %>% | ||
| # t() | ||
| mat_mouseLungLesions[1:5, 1:5] | ||
|
|
||
| meta_mouseLungLesions <- read_csv("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131957/suppl/GSE131957_single_cell_metadata.csv.gz") | ||
| meta_mouseLungLesions <- meta_mouseLungLesions %>% column_to_rownames("X1") %>% t() %>% as.data.frame() | ||
| meta2 <- meta_mouseLungLesions[colnames(mat_mouseLungLesions),] | ||
| meta_mouseLungLesions | ||
| sum(colnames(mat_mouseLungLesions) %in% meta_mouseLungLesions$cluster) | ||
| ncol(mat_mouseLungLesions) | ||
|
|
||
| source("~/Reference-Matrix-Generation/R/utils/utils.r") | ||
| checkRawCounts(as.matrix(mat_mouseLungLesions)) | ||
|
|
||
| GSE131957WTNaiveNormalized <- NormalizeData(mat_mouseLungLesions) | ||
|
|
||
| new_ref_matrix <- average_clusters(mat = GSE131957WTNaiveNormalized, metadata = meta2, cluster_col = "cluster_annotation", if_log = FALSE) | ||
| new_ref_matrix_hashed <- average_clusters(mat = mat_mouseLungLesions, metadata = meta_mouseLungLesions, if_log = FALSE) | ||
| head(new_ref_matrix) | ||
| tail(new_ref_matrix) | ||
| newcols <- sapply(colnames(new_ref_matrix_hashed), digest, algo = "sha1") | ||
| colnames(new_ref_matrix_hashed) <- newcols | ||
| head(new_ref_matrix_hashed) | ||
| tail(new_ref_matrix_hashed) | ||
| saveRDS(new_ref_matrix_hashed, "GSE131957Hashed.rds") | ||
| saveRDS(new_ref_matrix, "GSE131957Beadneg1.rds") |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,41 @@ | ||
| library(dplyr) | ||
| library(Seurat) | ||
| library(patchwork) | ||
| library(clustifyr) | ||
| library(tidyverse) | ||
| library(digest) | ||
| library(here) | ||
|
|
||
| proj_dir <- here() | ||
| GSE131957 <- file.path(proj_dir, "Reference-Matrix-Generation", "data", "GSE131957_Raw 2", "GSM3832738_wt_tumor_adt.csv.gz") | ||
|
|
||
| mat_mouseLungLesions <- read.csv(GSE131957) | ||
| mat_mouseLungLesions <- mat_mouseLungLesions %>% | ||
| # as.data.frame() %>% | ||
| column_to_rownames('X') | ||
| # as.matrix() %>% | ||
| # t() | ||
| mat_mouseLungLesions[1:5, 1:5] | ||
|
|
||
| meta_mouseLungLesions <- read_csv("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131957/suppl/GSE131957_single_cell_metadata.csv.gz") | ||
| meta_mouseLungLesions <- meta_mouseLungLesions %>% column_to_rownames("X1") %>% t() %>% as.data.frame() | ||
| meta2 <- meta_mouseLungLesions[colnames(mat_mouseLungLesions),] | ||
| meta_mouseLungLesions | ||
| sum(colnames(mat_mouseLungLesions) %in% meta_mouseLungLesions$cluster) | ||
| ncol(mat_mouseLungLesions) | ||
|
|
||
| source("~/Reference-Matrix-Generation/R/utils/utils.r") | ||
| checkRawCounts(as.matrix(mat_mouseLungLesions)) | ||
|
|
||
| GSE131957WTNaiveNormalized <- NormalizeData(mat_mouseLungLesions) | ||
|
|
||
| new_ref_matrix <- average_clusters(mat = GSE131957WTNaiveNormalized, metadata = meta2, cluster_col = "cluster_annotation", if_log = FALSE) | ||
| new_ref_matrix_hashed <- average_clusters(mat = mat_mouseLungLesions, metadata = meta_mouseLungLesions, if_log = FALSE) | ||
| head(new_ref_matrix) | ||
| tail(new_ref_matrix) | ||
| newcols <- sapply(colnames(new_ref_matrix_hashed), digest, algo = "sha1") | ||
| colnames(new_ref_matrix_hashed) <- newcols | ||
| head(new_ref_matrix_hashed) | ||
| tail(new_ref_matrix_hashed) | ||
| saveRDS(new_ref_matrix_hashed, "GSE131957Hashed.rds") | ||
| saveRDS(new_ref_matrix, "GSE131957WTTumorADT.rds") |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,41 @@ | ||
| library(dplyr) | ||
| library(Seurat) | ||
| library(patchwork) | ||
| library(clustifyr) | ||
| library(tidyverse) | ||
| library(digest) | ||
| library(here) | ||
|
|
||
| proj_dir <- here() | ||
| GSE131957 <- file.path(proj_dir, "Reference-Matrix-Generation", "data", "GSE131957_Raw 2", "GSM3832737_wt_tumor_gex.csv.gz") | ||
|
|
||
| mat_mouseLungLesions <- read.csv(GSE131957) | ||
| mat_mouseLungLesions <- mat_mouseLungLesions %>% | ||
| # as.data.frame() %>% | ||
| column_to_rownames('X') | ||
| # as.matrix() %>% | ||
| # t() | ||
| mat_mouseLungLesions[1:5, 1:5] | ||
|
|
||
| meta_mouseLungLesions <- read_csv("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131957/suppl/GSE131957_single_cell_metadata.csv.gz") | ||
| meta_mouseLungLesions <- meta_mouseLungLesions %>% column_to_rownames("X1") %>% t() %>% as.data.frame() | ||
| meta2 <- meta_mouseLungLesions[colnames(mat_mouseLungLesions),] | ||
| meta_mouseLungLesions | ||
| sum(colnames(mat_mouseLungLesions) %in% meta_mouseLungLesions$cluster) | ||
| ncol(mat_mouseLungLesions) | ||
|
|
||
| source("~/Reference-Matrix-Generation/R/utils/utils.r") | ||
| checkRawCounts(as.matrix(mat_mouseLungLesions)) | ||
|
|
||
| GSE131957WTNaiveNormalized <- NormalizeData(mat_mouseLungLesions) | ||
|
|
||
| new_ref_matrix <- average_clusters(mat = GSE131957WTNaiveNormalized, metadata = meta2, cluster_col = "cluster_annotation", if_log = FALSE) | ||
| new_ref_matrix_hashed <- average_clusters(mat = mat_mouseLungLesions, metadata = meta_mouseLungLesions, if_log = FALSE) | ||
| head(new_ref_matrix) | ||
| tail(new_ref_matrix) | ||
| newcols <- sapply(colnames(new_ref_matrix_hashed), digest, algo = "sha1") | ||
| colnames(new_ref_matrix_hashed) <- newcols | ||
| head(new_ref_matrix_hashed) | ||
| tail(new_ref_matrix_hashed) | ||
| saveRDS(new_ref_matrix_hashed, "GSE131957Hashed.rds") | ||
| saveRDS(new_ref_matrix, "GSE131957WTTumor.rds") |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,41 @@ | ||
| library(dplyr) | ||
| library(Seurat) | ||
| library(patchwork) | ||
| library(clustifyr) | ||
| library(tidyverse) | ||
| library(digest) | ||
| library(here) | ||
|
|
||
| proj_dir <- here() | ||
| GSE131957 <- file.path(proj_dir, "Reference-Matrix-Generation", "data", "GSE131957_Raw 2", "GSM3832735_wt_naive_gex.csv.gz") | ||
|
|
||
| mat_mouseLungLesions <- read.csv(GSE131957) | ||
| mat_mouseLungLesions <- mat_mouseLungLesions %>% | ||
| # as.data.frame() %>% | ||
| column_to_rownames('X') | ||
| # as.matrix() %>% | ||
| # t() | ||
| mat_mouseLungLesions[1:5, 1:5] | ||
|
|
||
| meta_mouseLungLesions <- read_csv("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131957/suppl/GSE131957_single_cell_metadata.csv.gz") | ||
| meta_mouseLungLesions <- meta_mouseLungLesions %>% column_to_rownames("X1") %>% t() %>% as.data.frame() | ||
| meta2 <- meta_mouseLungLesions[colnames(mat_mouseLungLesions),] | ||
| meta_mouseLungLesions | ||
| sum(colnames(mat_mouseLungLesions) %in% meta_mouseLungLesions$cluster) | ||
| ncol(mat_mouseLungLesions) | ||
|
|
||
| source("~/Reference-Matrix-Generation/R/utils/utils.r") | ||
| checkRawCounts(as.matrix(mat_mouseLungLesions)) | ||
|
|
||
| GSE131957WTNaiveNormalized <- NormalizeData(mat_mouseLungLesions) | ||
|
|
||
| new_ref_matrix <- average_clusters(mat = GSE131957WTNaiveNormalized, metadata = meta2, cluster_col = "cluster_annotation", if_log = FALSE) | ||
| new_ref_matrix_hashed <- average_clusters(mat = mat_mouseLungLesions, metadata = meta_mouseLungLesions, if_log = FALSE) | ||
| head(new_ref_matrix) | ||
| tail(new_ref_matrix) | ||
| newcols <- sapply(colnames(new_ref_matrix_hashed), digest, algo = "sha1") | ||
| colnames(new_ref_matrix_hashed) <- newcols | ||
| head(new_ref_matrix_hashed) | ||
| tail(new_ref_matrix_hashed) | ||
| saveRDS(new_ref_matrix_hashed, "GSE131957Hashed.rds") | ||
| saveRDS(new_ref_matrix, "GSE131957.rds") |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,41 @@ | ||
| library(dplyr) | ||
| library(Seurat) | ||
| library(patchwork) | ||
| library(clustifyr) | ||
| library(tidyverse) | ||
| library(digest) | ||
| library(here) | ||
|
|
||
| proj_dir <- here() | ||
| GSE131957 <- file.path(proj_dir, "Reference-Matrix-Generation", "data", "GSE131957_Raw 2", "GSM3832736_wt_naive_adt.csv.gz") | ||
|
|
||
| mat_mouseLungLesions <- read.csv(GSE131957) | ||
| mat_mouseLungLesions <- mat_mouseLungLesions %>% | ||
| # as.data.frame() %>% | ||
| column_to_rownames('X') | ||
| # as.matrix() %>% | ||
| # t() | ||
| mat_mouseLungLesions[1:5, 1:5] | ||
|
|
||
| meta_mouseLungLesions <- read_csv("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131957/suppl/GSE131957_single_cell_metadata.csv.gz") | ||
| meta_mouseLungLesions <- meta_mouseLungLesions %>% column_to_rownames("X1") %>% t() %>% as.data.frame() | ||
| meta2 <- meta_mouseLungLesions[colnames(mat_mouseLungLesions),] | ||
| meta_mouseLungLesions | ||
| sum(colnames(mat_mouseLungLesions) %in% meta_mouseLungLesions$cluster) | ||
| ncol(mat_mouseLungLesions) | ||
|
|
||
| source("~/Reference-Matrix-Generation/R/utils/utils.r") | ||
| checkRawCounts(as.matrix(mat_mouseLungLesions)) | ||
|
|
||
| GSE131957WTNaiveNormalized <- NormalizeData(mat_mouseLungLesions) | ||
|
|
||
| new_ref_matrix <- average_clusters(mat = GSE131957WTNaiveNormalized, metadata = meta2, cluster_col = "cluster_annotation", if_log = FALSE) | ||
| new_ref_matrix_hashed <- average_clusters(mat = mat_mouseLungLesions, metadata = meta_mouseLungLesions, if_log = FALSE) | ||
| head(new_ref_matrix) | ||
| tail(new_ref_matrix) | ||
| newcols <- sapply(colnames(new_ref_matrix_hashed), digest, algo = "sha1") | ||
| colnames(new_ref_matrix_hashed) <- newcols | ||
| head(new_ref_matrix_hashed) | ||
| tail(new_ref_matrix_hashed) | ||
| saveRDS(new_ref_matrix_hashed, "GSE131957Hashed.rds") | ||
| saveRDS(new_ref_matrix, "GSE131957WTNaiveADT.rds") |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,41 @@ | ||
| library(dplyr) | ||
| library(Seurat) | ||
| library(patchwork) | ||
| library(clustifyr) | ||
| library(tidyverse) | ||
| library(digest) | ||
| library(here) | ||
|
|
||
| proj_dir <- here() | ||
| GSE131957 <- file.path(proj_dir, "Reference-Matrix-Generation", "data", "GSE131957_Raw 2", "GSM3832739_ccr7ko_naive_gex.csv.gz") | ||
|
|
||
| mat_mouseLungLesions <- read.csv(GSE131957) | ||
| mat_mouseLungLesions <- mat_mouseLungLesions %>% | ||
| # as.data.frame() %>% | ||
| column_to_rownames('X') | ||
| # as.matrix() %>% | ||
| # t() | ||
| mat_mouseLungLesions[1:5, 1:5] | ||
|
|
||
| meta_mouseLungLesions <- read_csv("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131957/suppl/GSE131957_single_cell_metadata.csv.gz") | ||
| meta_mouseLungLesions <- meta_mouseLungLesions %>% column_to_rownames("X1") %>% t() %>% as.data.frame() | ||
| meta2 <- meta_mouseLungLesions[colnames(mat_mouseLungLesions),] | ||
| meta_mouseLungLesions | ||
| sum(colnames(mat_mouseLungLesions) %in% meta_mouseLungLesions$cluster) | ||
| ncol(mat_mouseLungLesions) | ||
|
|
||
| source("~/Reference-Matrix-Generation/R/utils/utils.r") | ||
| checkRawCounts(as.matrix(mat_mouseLungLesions)) | ||
|
|
||
| GSE131957WTNaiveNormalized <- NormalizeData(mat_mouseLungLesions) | ||
|
|
||
| new_ref_matrix <- average_clusters(mat = GSE131957WTNaiveNormalized, metadata = meta2, cluster_col = "cluster_annotation", if_log = FALSE) | ||
| new_ref_matrix_hashed <- average_clusters(mat = mat_mouseLungLesions, metadata = meta_mouseLungLesions, if_log = FALSE) | ||
| head(new_ref_matrix) | ||
| tail(new_ref_matrix) | ||
| newcols <- sapply(colnames(new_ref_matrix_hashed), digest, algo = "sha1") | ||
| colnames(new_ref_matrix_hashed) <- newcols | ||
| head(new_ref_matrix_hashed) | ||
| tail(new_ref_matrix_hashed) | ||
| saveRDS(new_ref_matrix_hashed, "GSE131957Hashed.rds") | ||
| saveRDS(new_ref_matrix, "GSE131957ccr7koNaive.rds") |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,41 @@ | ||
| library(dplyr) | ||
| library(Seurat) | ||
| library(patchwork) | ||
| library(clustifyr) | ||
| library(tidyverse) | ||
| library(digest) | ||
| library(here) | ||
|
|
||
| proj_dir <- here() | ||
| GSE131957 <- file.path(proj_dir, "Reference-Matrix-Generation", "data", "GSE131957_Raw 2", "GSM3832740_ccr7ko_naive_adt.csv.gz") | ||
|
|
||
| mat_mouseLungLesions <- read.csv(GSE131957) | ||
| mat_mouseLungLesions <- mat_mouseLungLesions %>% | ||
| # as.data.frame() %>% | ||
| column_to_rownames('X') | ||
| # as.matrix() %>% | ||
| # t() | ||
| mat_mouseLungLesions[1:5, 1:5] | ||
|
|
||
| meta_mouseLungLesions <- read_csv("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131957/suppl/GSE131957_single_cell_metadata.csv.gz") | ||
| meta_mouseLungLesions <- meta_mouseLungLesions %>% column_to_rownames("X1") %>% t() %>% as.data.frame() | ||
| meta2 <- meta_mouseLungLesions[colnames(mat_mouseLungLesions),] | ||
| meta_mouseLungLesions | ||
| sum(colnames(mat_mouseLungLesions) %in% meta_mouseLungLesions$cluster) | ||
| ncol(mat_mouseLungLesions) | ||
|
|
||
| source("~/Reference-Matrix-Generation/R/utils/utils.r") | ||
| checkRawCounts(as.matrix(mat_mouseLungLesions)) | ||
|
|
||
| GSE131957WTNaiveNormalized <- NormalizeData(mat_mouseLungLesions) | ||
|
|
||
| new_ref_matrix <- average_clusters(mat = GSE131957WTNaiveNormalized, metadata = meta2, cluster_col = "cluster_annotation", if_log = FALSE) | ||
| new_ref_matrix_hashed <- average_clusters(mat = mat_mouseLungLesions, metadata = meta_mouseLungLesions, if_log = FALSE) | ||
| head(new_ref_matrix) | ||
| tail(new_ref_matrix) | ||
| newcols <- sapply(colnames(new_ref_matrix_hashed), digest, algo = "sha1") | ||
| colnames(new_ref_matrix_hashed) <- newcols | ||
| head(new_ref_matrix_hashed) | ||
| tail(new_ref_matrix_hashed) | ||
| saveRDS(new_ref_matrix_hashed, "GSE131957Hashed.rds") | ||
| saveRDS(new_ref_matrix, "GSE131957ccr7koNaiveADT.rds") |
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
If we still use the hashed versions, then if_log also needs to be changed
Uh oh!
There was an error while loading. Please reload this page.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
@raysinensis Do you mean just change it to
FALSEon line 37?