I really am a noob using forloops. I have created 13 clusters using Seurat and now i would like to compare cluster 8 to all other clusters. I am managing to do this manually but the use of a for loop would be really nice. i think i would then have to specify a for loop for ident.2. I however do not really know how to run it. The code i am running to get one comparison right now is:
cluster8filt.markers <- FindMarkers(UMAP_Llan, ident.1 = 8, ident.2 = 5, min.pct = 0.25, logfc.treshold = (0.585 | -0.585))
#add gene symbols to the DE table
markers.8filt <- tibble::rownames_to_column(cluster8filt.markers, "value")
colnames(markers.8filt) <- c("gene","p value" ,"avglog2FC", "pct.1", "pct.2", "p_val_adj")
#filter out P>0.1
markers.8.p0.1 <- subset(markers.8filt, p_val_adj <0.1 )
#export to excel
write_xlsx(markers.8.p0.1,"C://Users//famvi//stage2//projecten//8vsallfilt.xlsx")
How do i specify then the ident.2 in a forloop? without losing all the other aspects as well.
I've already tried this option (even not filtering on log2FC and p value), but it did not work for me:
for (i in 0:12){
marker8vs_i <- FindMarkers(UMAP_Llan, ident.1 = 8, ident.2 = i, min.pct = 0.25, logfc.treshold = (0.585 | -0.585))
filename <- paste0("8vs", i,".xlsx")
print(filename)
write_xlsx(marker_i, filename,"C://Users//famvi//stage2//projecten//lala.xlsx")
}
Also, i see now that logfc.treshold is also not working lol idk why
I have a dataframe where all information is in one row. see picture below
untidy data
I need to change it to something like this
tidy data
so the first value (suffix_name) in the row should be changed to a variable and the second value (none) should be first value of new variable (suffix_name)
please see images
with the following code you can split the information of the row.
You need to use the library data.table to subset the vars or values columns.
library(data.table)
data_raw.dt <- data.table(
V2_00011 = "'SUFFIX_NAME'",
V2_00012 = 'NONE}}',
V2_00013 = "'PATIENT_ID'",
V2_00014 = "'CZMIl1844982497'",
V2_00015 = "'BIRTH_DATE'",
V2_00016 = "'1987-01-01'",
V2_00017 = "'GENDER'",
V2_00018 = "'Unknown'",
V2_00019 = "'OBSCURITY_LEVEL'",
V2_00020 = "'Normal'")
vars <- seq(1, ncol(data_raw.dt), by = 2)
vals <- seq(2, ncol(data_raw.dt), by = 2)
data_ref.dt <- data.table(matrix(data_raw.dt[, ..vals], ncol = length(vals)))
names(data_ref.dt) <- paste(data_raw.dt[, ..vars])
Here you can see the results.
print(data_raw.dt)
V2_00011 V2_00012 V2_00013 V2_00014 V2_00015 V2_00016 V2_00017 V2_00018 V2_00019 V2_00020
'SUFFIX_NAME' NONE}} 'PATIENT_ID' 'CZMIl1844982497' 'BIRTH_DATE' '1987-01-01' 'GENDER' 'Unknown' 'OBSCURITY_LEVEL' 'Normal'
print(data_ref.dt)
'SUFFIX_NAME' 'PATIENT_ID' 'BIRTH_DATE' 'GENDER' 'OBSCURITY_LEVEL'
NONE}} 'CZMIl1844982497' '1987-01-01' 'Unknown' 'Normal'
I have 24 variables called empl_1 -empl_24 (e.g. empl_2; empl_3..)
I would like to write a loop in R that takes this values 1-24 and puts them in the respective places so the corresponding variables are either called or created with i = 1-24. The sample below shows what I would like to have within the loop (e.g. ye1- ye24; ipw_atet_1 - ipw_atet_14 and so on.
ye1_ipw <- empl$empl_1[insample==1]
ipw_atet_1 <- treatweight(y=ye1_ipw, d=treat_ipw, x=x1_ipw, ATET =TRUE, trim=0.05, boot = 2)
ipw_atet_1
ipw_atet_1$se
ye2_ipw <- empl$empl_2[insample==1]
ipw_atet_2 <- treatweight(y=ye2_ipw, d=treat_ipw, x=x1_ipw, ATET =TRUE, trim=0.05, boot = 2)
ipw_atet_2
ipw_atet_2$se
ye3_ipw <- empl$empl_3[insample==1]
ipw_atet_3 <- treatweight(y=ye3_ipw, d=treat_ipw, x=x1_ipw, ATET =TRUE, trim=0.05, boot = 2)
ipw_atet_3
ipw_atet_3$se
coming from a Stata environment I tried
for (i in seq_anlong(empl_list)){
ye[i]_ipw <- empl$empl_[i][insample==1]
ipw_atet_[i]<-treatweight(y=ye[i]_ipw, d=treat_ipw, x=x1_ipw, ATET=TRUE, trim=0.05, boot =2
}
However this does not work at all. Do you have any idea how to approach this problem by writing a nice loop? Thank you so much for your help =)
You can try with lapply :
result <- lapply(empl[paste0('empl_', 1:24)], function(x)
treatweight(y = x[insample==1], d = treat_ipw,
x = x1_ipw, ATET = TRUE, trim = 0.05, boot = 2))
result would be a list output storing the data of all the 24 variables in same object which is easier to manage and process instead of having different vectors.
I'm trying to create a for loop in R to iterate through a list of genetic variants, labeled with rsID's, and filter the results by patient ID.
ace2_snps <- c("rs4646121", "rs4646127", "rs1996225", "rs2158082", "rs4830974", "rs148271868", "rs113539251", "rs4646135", "rs4646179", "rs2301693", "rs16980031", "rs12689012", "rs4646141", "rs142049267", "rs16979971", "rs12007623", "rs4646182", "rs147214574", "rs6632677", "rs139469582", "rs149000434", "rs148805807", "rs112032651", "rs144314464", "rs147077778", "rs182259051", "rs112621533", "rs35803318", "rs35304868", "rs113848176", "rs145345877", "rs12009805", "rs233570", "rs73635824", "rs73635823", "rs4646142", "rs4646157", "rs2074192", "rs79878075", "rs144239059", "rs67635467", "rs183583165", "rs137910448", "rs116419580", "rs2097723", "rs4646170")
for (snps in ace2_snps) {
genotype_snps <- as.data.frame(bgen_ACE2$data[snps,,])
idfromcsv <- read.csv("/Users/keeseyyyyy/Desktop/Walley/pospatid.csv")
id <- as.character(idfromcsv[[1]])
filtered_snps <- genotype_snps[id,] }
I need to run genotype_rs146217251 <- as.data.frame(bgen_ACE2$data["rs146217251",,]) for each rsID, and then I'd like to label the variable filtered_snps according to its rsID in the place of "snps" in the variable name for each variant.
I'm not very familiar with R syntax. Can anyone give me some tips?
For one variant, the process would go like this:
genotype_rs146217251 <- as.data.frame(bgen_ACE2$data["rs146217251",,])
idfromcsv <- read.csv("/Users/keeseyyyyy/Desktop/Walley/pospatid.csv")
id <- as.character(idfromcsv[[1]])
filtered <- genotype_rs146217251[id,]
I have the following sample dataset (below and/or as CSVs here: http://goo.gl/wK57T) which I want to transform as follows. For each person in a household I want to create two new variables OrigTAZ and DestTAZ. It should take the value in TripendTAZ and put that in DestTAZ. For OrigTAZ it should put value of TripendTAZ from the previous row. For the first trip of every person in a household (Tripid = 1) the OrigTAZ = hometaz. For each person in a household, from the second trip OrigTAZ = TripendTAZ_(n-1) and DestTAZ = TripEndTAZ. The sample input and output data are shown below. I tried the suggestions shown here: Basic lag in R vector/dataframe but have not had luck. I am used to doing something like this in SAS.
Any help is appreciated.
TIA,
Krishnan
SAS Code Sample
if Houseid = lag(Houseid) then do;
if Personid = lag(Personid) then do;
DestTAZ = TripendTAZ;
if Tripid = 1 then OrigTAZ = hometaz
else
OrigTAZ = lag(TripendTAZ);
end;
end;
INPUT DATA
Houseid,Personid,Tripid,hometaz,TripendTAZ
1,1,1,45,4
1,1,2,45,7
1,1,3,45,87
1,1,4,45,34
1,1,5,45,45
2,1,1,8,96
2,1,2,8,4
2,1,3,8,2
2,1,4,8,1
2,1,5,8,8
2,2,1,8,58
2,2,2,8,67
2,2,3,8,9
2,2,4,8,10
2,2,5,8,8
3,1,1,7,89
3,1,2,7,35
3,1,3,7,32
3,1,4,7,56
3,1,5,7,7
OUTPUT DATA
Houseid,Personid,Tripid,hometaz,TripendTAZ,OrigTAZ,DestTAZ
1,1,1,45,4,45,4
1,1,2,45,7,4,7
1,1,3,45,87,7,87
1,1,4,45,34,87,34
1,1,5,45,45,34,45
2,1,1,8,96,8,96
2,1,2,8,4,96,4
2,1,3,8,2,4,2
2,1,4,8,1,2,1
2,1,5,8,8,1,8
2,2,1,8,58,8,58
2,2,2,8,67,58,67
2,2,3,8,9,67,9
2,2,4,8,10,9,10
2,2,5,8,8,10,8
3,1,1,7,89,7,89
3,1,2,7,35,89,35
3,1,3,7,32,35,32
3,1,4,7,56,32,56
3,1,5,7,7,56,7
Just proceed through the steps you outlined step-by-step and it isn't so bad.
First I'll read in your data by copying it:
df <- read.csv(file('clipboard'))
Then I'll sort to make sure the data frame is ordered by houseid, then personid, then tripid:
# first sort so that it's ordered by Houseid, then Personid, then Tripid:
df <- with(df, df[order(Houseid,Personid,Tripid),])
Then follow the steps you specified:
# take value in TripendTAZ and put it in DestTAZ
df$DestTAZ <- df$TripendTAZ
# Set OrigTAZ = value from previous row
df$OrigTAZ <- c(NA,df$TripendTAZ[-nrow(df)])
# For the first trip of every person in a household (Tripid = 1),
# OrigTAZ = hometaz.
df$OrigTAZ[ df$Tripid==1 ] <- df$hometaz[ df$Tripid==1 ]
You'll notice that df is then what you're after.