Create a table from dataframe column values mean and standard deviation in R
I am new to R so no idea about the code. I have two data frames. One dataframe looks like this.
df
ID | Disease |
---|---|
GSM239170 | Control |
GSM239323 | Control |
GSM239324 | Control |
GSM239326 | Control |
GSM239328 | AML |
GSM239329 | AML |
GSM239331 | AML |
GSM239332 | Control |
GSM239333 | Control |
And the other dataframe looks like this:
df1
GSM239170 | GSM239323 | GSM239324 | GSM239326 | GSM239328 | GSM239329 | GSM239331 | GSM239332 | GSM239333 |
---|---|---|---|---|---|---|---|---|
3.016704177 | 3.285669072 | 2.929482692 | 2.922820483 | 3.15950317 | 3.163327169 | 2.985901308 | 3.122708843 | 3.070948463 |
7.977735461 | 6.532514237 | 6.388007183 | 6.466679556 | 6.432795021 | 6.407321524 | 6.426470803 | 6.376394357 | 6.469070308 |
4.207280707 | 4.994965767 | 4.40159671 | 4.747114589 | 4.830045513 | 4.213762092 | 4.884418365 | 4.4318876 | 4.849665444 |
7.25609471 | 7.420807337 | 6.999340125 | 7.094488581 | 7.024332721 | 7.17928981 | 7.159898654 | 7.009977785 | 6.830979234 |
2.204955099 | 2.331625217 | 2.133305231 | 2.18332885 | 2.12778313 | 2.269697813 | 2.264705552 | 2.253940441 | 2.287924323 |
7.28437278 | 6.983593721 | 6.86337111 | 6.865970678 | 7.219840938 | 7.181113053 | 7.392230178 | 7.484052914 | 7.52498281 |
4.265792764 | 4.970684112 | 4.595545125 | 4.575545289 | 4.547957809 | 4.68215122 | 4.674495889 | 4.675841709 | 4.643311767 |
2.6943516 | 2.916324936 | 2.578130269 | 2.659717988 | 2.567436676 | 2.8095128 | 2.790110381 | 2.795882913 | 2.884588792 |
3.646303109 | 8.817891552 | 11.4248793 | 10.74738082 | 9.296043108 | 9.53150669 | 8.285160496 | 9.769919327 | 9.774610531 |
3.040292001 | 3.38486713 | 2.958851115 | 3.047880699 | 2.878562717 | 3.209319974 | 3.20260379 | 3.195993624 | 3.3004227 |
2.357625231 | 2.444753172 | 2.340767158 | 2.32143889 | 2.282608342 | 2.401218719 | 2.385568421 | 2.375334953 | 2.432634747 |
5.378494673 | 6.065038394 | 5.134842087 | 5.367342376 | 5.682051149 | 5.712072512 | 5.57179966 | 5.72082395 | 5.656674512 |
2.833814735 | 3.038434511 | 2.837711812 | 2.859800224 | 2.866040813 | 2.969167906 | 2.929449968 | 2.963530689 | 2.931065261 |
6.192932281 | 6.478439634 | 6.180169144 | 6.151689376 | 6.238949956 | 6.708196123 | 6.441437631 | 6.448280595 | 6.413562269 |
4.543042482 | 4.786227217 | 4.445131477 | 4.51471011 | 4.491645167 | 4.460114204 | 4.602482637 | 4.587221948 | 4.623125028 |
6.069437462 | 6.232738284 | 6.74644117 | 7.04995802 | 6.938928532 | 6.348253102 | 6.080950712 | 6.324619355 | 6.472893789 |
I want to make a table to include mean_AML, sd_AML (standard deviation), min_AML, max_AML, mean_Control, sd_Control, min_Control, max_Control, and Fold_change (i.e, mean_AML – mean_Control) for each gene. It is fine to use built-in functions.
Can't figure out the way how I can do this. Please help.
Thanks.
--- UPDATE ---
Hints: split the dataset into AML data and normal data sets, and then for each gene/probeset, calculate its mean, standard derivation, min and max expression values across samples separately (using a built-in function), and further merge these statistical values for each gene into one table. Apply data.frame() and give the created table the same row names as the gene expression data table.
Another option with old function tidyr::gather
to have a column df:
library(tidyverse)
df2_spread <- df1 %>%
tidyr::gather(ID, val) %>%
left_join(df, by = 'ID')
result_1 <- df2_spread %>%
group_by(Disease, gene = ID) %>%
summarise(n = n(),
mean = mean(val),
sd = sd(val),
min = min(val),
max = max(val), .groups = "drop")
A tibble: 9 × 7
Disease gene n mean sd min max
<chr> <chr> <int> <dbl> <dbl> <dbl> <dbl>
1 AML GSM239328 16 4.91 2.15 2.13 9.30
2 AML GSM239329 16 4.95 2.13 2.27 9.53
3 AML GSM239331 16 4.88 1.96 2.26 8.29
4 Control GSM239170 16 4.56 1.91 2.20 7.98
5 Control GSM239323 16 5.04 1.98 2.33 8.82
6 Control GSM239324 16 4.93 2.45 2.13 11.4
7 Control GSM239326 16 4.97 2.34 2.18 10.7
8 Control GSM239332 16 4.97 2.16 2.25 9.77
9 Control GSM239333 16 5.01 2.14 2.29 9.77
In any case I'm not able to find a way to calculate Fold_change for each gene since there seems to be only one disease by gene here.
Here are the datas
df <- tibble::tribble(
~ID, ~Disease,
"GSM239170", "Control",
"GSM239323", "Control",
"GSM239324", "Control",
"GSM239326", "Control",
"GSM239328", "AML",
"GSM239329", "AML",
"GSM239331", "AML",
"GSM239332", "Control",
"GSM239333", "Control"
)
df1 <- tibble::tribble(
~GSM239170, ~GSM239323, ~GSM239324, ~GSM239326, ~GSM239328, ~GSM239329, ~GSM239331, ~GSM239332, ~GSM239333,
3.016704177, 3.285669072, 2.929482692, 2.922820483, 3.15950317, 3.163327169, 2.985901308, 3.122708843, 3.070948463,
7.977735461, 6.532514237, 6.388007183, 6.466679556, 6.432795021, 6.407321524, 6.426470803, 6.376394357, 6.469070308,
4.207280707, 4.994965767, 4.40159671, 4.747114589, 4.830045513, 4.213762092, 4.884418365, 4.4318876, 4.849665444,
7.25609471, 7.420807337, 6.999340125, 7.094488581, 7.024332721, 7.17928981, 7.159898654, 7.009977785, 6.830979234,
2.204955099, 2.331625217, 2.133305231, 2.18332885, 2.12778313, 2.269697813, 2.264705552, 2.253940441, 2.287924323,
7.28437278, 6.983593721, 6.86337111, 6.865970678, 7.219840938, 7.181113053, 7.392230178, 7.484052914, 7.52498281,
4.265792764, 4.970684112, 4.595545125, 4.575545289, 4.547957809, 4.68215122, 4.674495889, 4.675841709, 4.643311767,
2.6943516, 2.916324936, 2.578130269, 2.659717988, 2.567436676, 2.8095128, 2.790110381, 2.795882913, 2.884588792,
3.646303109, 8.817891552, 11.4248793, 10.74738082, 9.296043108, 9.53150669, 8.285160496, 9.769919327, 9.774610531,
3.040292001, 3.38486713, 2.958851115, 3.047880699, 2.878562717, 3.209319974, 3.20260379, 3.195993624, 3.3004227,
2.357625231, 2.444753172, 2.340767158, 2.32143889, 2.282608342, 2.401218719, 2.385568421, 2.375334953, 2.432634747,
5.378494673, 6.065038394, 5.134842087, 5.367342376, 5.682051149, 5.712072512, 5.57179966, 5.72082395, 5.656674512,
2.833814735, 3.038434511, 2.837711812, 2.859800224, 2.866040813, 2.969167906, 2.929449968, 2.963530689, 2.931065261,
6.192932281, 6.478439634, 6.180169144, 6.151689376, 6.238949956, 6.708196123, 6.441437631, 6.448280595, 6.413562269,
4.543042482, 4.786227217, 4.445131477, 4.51471011, 4.491645167, 4.460114204, 4.602482637, 4.587221948, 4.623125028,
6.069437462, 6.232738284, 6.74644117, 7.04995802, 6.938928532, 6.348253102, 6.080950712, 6.324619355, 6.472893789
)
We could combine pivot_longer
with right_join
and then use summarise
on the group:
library(dplyr)
library(tidyr)
df1 %>%
pivot_longer(
everything(),
names_to = "ID",
values_to = "value"
) %>%
right_join(df, by="ID") %>%
group_by(Disease) %>%
summarise(Min = min(value), Mean = mean(value), Max = max(value), Sd = sd(value)) %>%
ungroup()
Disease Min Mean Max Sd
<chr> <dbl> <dbl> <dbl> <dbl>
1 AML 2.13 4.91 9.53 2.04
2 Control 2.13 4.92 11.4 2.12