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Ependymoma subtyping #490

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Feb 18, 2020
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34cd0a8
Initial files added to ependymoma subtyping folder
Jan 29, 2020
25228f2
Added bash script and changed the paths for all files to run from Ope…
Jan 30, 2020
9313bda
Added bash script and changed the paths for all files to run from Ope…
Jan 30, 2020
24d8a6f
Add Ependymoma subtyping to CI
jashapiro Feb 3, 2020
fb09448
Merge branch 'master' into ependymoma_subtyping
jashapiro Feb 3, 2020
8f80aec
Add to analyses/README.md
jashapiro Feb 3, 2020
5c5119c
Test removing rpy2 and using pyreadr exclusively
jashapiro Feb 3, 2020
5d4c32c
Change to use pyreadr properly
jashapiro Feb 3, 2020
e55ea34
Revert pyreadr changes
jashapiro Feb 3, 2020
1491b2d
Add subset flag to CI
jashapiro Feb 4, 2020
4d83601
Use R to generate subset file & shell to specify filenames
jashapiro Feb 4, 2020
5f119b1
Add results file
jashapiro Feb 4, 2020
408c02c
Move Ependymoma subtyping up in CI
jashapiro Feb 4, 2020
d02c4d0
Responding to pull request reviews
Feb 6, 2020
ba0e00a
Adding jupyter notebook
Feb 6, 2020
b5d1a77
Merge branch 'ependymoma_subtyping' of https://github.com/tkoganti/Op…
Feb 6, 2020
91d0b76
Typo fixes
jashapiro Feb 7, 2020
e842b27
Merge branch 'master' into ependymoma_subtyping
jashapiro Feb 7, 2020
e5f3a1e
Update gistic filename
jashapiro Feb 7, 2020
6713c70
Changed implemented as suggested on feb 7 2020
Feb 10, 2020
e742aaf
Small review changes
jashapiro Feb 10, 2020
aca978b
Update 00-subset-for-EPN.R with changes from @cansavvy code review
jashapiro Feb 10, 2020
d9c44d6
Zscore column names changed
Feb 10, 2020
f68966a
Changed how merge is done between RNA and DNA tables
Feb 10, 2020
415b5e7
Removed comment lines
Feb 10, 2020
3100358
remove duplicate commented code.
jashapiro Feb 10, 2020
33bacc2
Merge branch 'master' into ependymoma_subtyping
jashapiro Feb 10, 2020
141183c
Added some columns as per comments from 02-12-2020
Feb 13, 2020
6bfb636
Merge remote-tracking branch 'upstream/master' into ependymoma_subtyping
jashapiro Feb 13, 2020
e81a424
update invocation of 02_ependymoma_generate_all_data.py
jashapiro Feb 13, 2020
20cda5f
Handle missing data, and some refactoring
jashapiro Feb 14, 2020
57884c5
Delete unused full table zscore
jashapiro Feb 14, 2020
d65e360
Merge remote-tracking branch 'upstream/master' into ependymoma_subtyping
jashapiro Feb 18, 2020
5d05922
Rerun with updated data
jashapiro Feb 18, 2020
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remove duplicate commented code.
  • Loading branch information
jashapiro authored Feb 10, 2020
commit 3100358167aa8702b5f7e602ae6f3183c1972891
Original file line number Diff line number Diff line change
Expand Up @@ -72,12 +72,7 @@ def DNA_samples_fill_df(row, CNA, arm, loss_gain):
return(0)

# Function to generate Z-scores column for every gene
#def fill_df_with_fpkm_zscores(df,fpkmdf, column_name, gene_name):
# zscore_list = stats.zscore(np.array(df.apply(lambda x: fpkmdf.loc[gene_name, x["Kids_First_Biospecimen_ID_RNA"]], axis=1)))
# df[column_name] = pd.Series(zscore_list)
# return(df)

def fill_df_with_fpkm_zscores(df,fpkmdf, gene_name):
def fill_df_with_fpkm_zscores(df, fpkmdf, gene_name):
zscore_list = stats.zscore(np.array(df.apply(lambda x: fpkmdf.loc[gene_name, x["Kids_First_Biospecimen_ID_RNA"]], axis=1)))
column_name = gene_name + "_expr_zscore"
df[column_name] = pd.Series(zscore_list)
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